There's alot to comment on here, so instead of doing the multi-quote thing, I'll just add my comments in red. I'll be cutting and pasting some comments together so that I may respond to them together.
The only time it looks like the cost will be an issue is when Con damage comes into play or level 1. I'd assume you just lose BP equal to the change in Con mod X levels, but that's something you may wish to mention when Con starts changing. I'll need to do that, thanks.
SpoilerShowAnimal Companion is solidly good for the same reasons it's good for a Druid. I would maybe decrease it down to BW Level-3, minimum one. If a BW really wanted to, then they could spend a feat to get it up to their character level. I'll think about that (particulary since everyone else has had the same comment.
The Arctic/Desert Adaptation is also interesting. I would, however, mention that you gain all of the lesser abilities if you spend more BP. This way, you've got the Endure Effect up at all times even if you went a little heavy to get energy resistance. Done.
Calm Animals is a little underwhelming as the only effect. May add something else? Not too sure there. Nor I, to be honest.
You may want to turn "Catfall (Su)" into Catfall (PLA). Also, you have it as "instant action" where I think you mean immediate. I copied Catfall directly from the SRD (sovelior_sage). I did make the change to Immediate, though.
See below for comments on the skill-boosting abilities.
Discern North is near worthless. All characters with 5 ranks in Survival can do that for free. But can they do it in a dungeon/castle/etc? I did think that this was a weak ability, but I was just filling in abilities that animals have. Maybe adding some type of ability to keep from getting lost?
Healthy as a Horse is also kind of underwhelming. It's not stated, but I'm inclined to assume it protects against magical diseases as well. Mix Serpent Blooded with Healthy as a Horse maybe? Poisons are probably more likely to show up than diseases, but bonus to one usually come with bonuses to the other. Done.
For Lesser Scent, do you just mean Scent? RAW, I am not familiar with anything called Lesser Scent. Other than that, looks fine. It's from Sean K. Reynolds' Curse of the Moon. I added the text along with a link under lesser scent. It had been my understanding that many people found scent to be too powerful for low-level characters. I'll do some thinking on it.
Natural Armor feels like something to grab when nothing else strikes your fancy. Basically a free feat, so, not bad.
I love Plating, but you need to clarify the initial Max Dex restriction on it. As is, it sounds like you start with NI Max Dex for the first cost, then go down to -1 Max Dex, which is silly and a little counter-intuitive. I also like how the extra BP further increase the duration. Removed the whole max Dex thing.
Savagery I: I'd almost want to say "add +1d4 damage..." for the next round with your natural weapons. It'd be a little extra incentive to take this for those guys who grabbed claws or tentacles is all. Otherwise, it shouldn't be an issue as it is a first level power. Added "for all your natural attacks this round" to all the Savagerys.
Track is a little underwhelming. In the case of Natural Armor, you're getting either an epic feat (not really) or an otherwise difficult to qualify monstrous feat (assuming you don't already have a natural armor score of at least +1). I don't know that anything else can be done to improve it. It is a feat, after all.
Venom looks okay, but it needs an initiation action. I also feel that, without some significant bonuses for having a higher wisdom score, the use of wisdom over constitution for the save feels forced. May just be me. This ability is missing the initiation action, however. Is it standard, move or swift? Fixed the initiation action. As for using Wisdom -- I'm using it as the "casting stat" for these abilities, so I've based the DC on it for that reason.
Wild Empathy feels kind of like Track. Doesn't really do much, but may be used to get into an odd PrC or two. Other than that, it feels like filler. It fits the flavor of the class. And I'm thinking of adding some other abilities that build upon it. Though perhaps I should add Calm Animals under this?
The insane amount of skill boosters here kind of saddens me, especially without some sort of additional benefit other than +more. Factoring the fact that this guys can get pretty high DCs for just a little bit extra makes them look like chumps compared to Incarnum-users who get to throw around their similar skill boosting levels for free all day without locking them out of combat abilities. From what I recall, Incarnum users have to lock Essentia into feats to get those bonuses. However, I did make upgrades to all of the skill boosters. I increased the duration to 1 hour/level, and added other niceties to most of them. I'll highlight those in a separate post.
As is, it looks like a level 1 Beast Warrior would grab Animal Companion at first level and then kind of not have any other class features. A simple remedy would be to give them 3 instead of 1 ability at first level, then go back down to 2 for the remaining level. Basically every system in DND operates like that. Martial Adepts get 3-6 maneuvers at first level, then down to just a few every other level afterwards. Incarnates and Totemists (Soulborns don't count) get a few soulmelds for the day to start before gaining more. You get the idea. I may end up giving them two abilities at 1st level. I don't what to do more for fear of dipping.
Rapid Healer looks a little lonely here. The 1/day limitation is also saddening. Maybe gain extra uses for extra BP? Also, you should mention that it's a standard healing rate for one complete night's of rest. Rapid healer was a repost of the Rapid Metabolism feat. It is a CHANGE to your normal healing, not a healing boost. I've clarified that language.
The DR/silver looks great when you can first get it, then decreases rapidly in effectiveness. Although, hey, the first time you get it, it's a guaranteed -1 to damage taken from most weapons! I'd probably have this start at DR 5, then work up at a lower increment. +2 or 3, probably. I've upgraded it to +2 per selection. I'm not sure about increasing it further. If I recall correctly, it should also allow your natural weapons to bypass silver DR.
Endurance is a feat. Also a bland one, but, it does open the door to Steadfast Determination... except you actually would probably have an acceptable Wisdom score. Maybe throw Diehard on here, too. Not like it's going to overpower someone. Endurance is also gained by the Ranger at this level, and I think I'll leave it as-is.
Fast Movement looks fine if other abilities start to provide some skirmish capabilities. I'm hoping they will.
Woodland Stride is okay. Not a terribly good or bad class ability, just kind of there. Awful handy for a detected scout trying to outpace his pursuers. But again, the Druid and Ranger got it, and it fits the flavor.
The abilities are starting to get interesting. Only thing I can really complain about is having so many of them take a standard action. I do not feel it would be too much to have most of these combat abilities be swifts to activate. Changed most of them to swifts.
SpoilerShowAnimal Affinity is probably good as an insight bonus, considering that once you choose a power, it's there for life. Increased the duration to 10 minutes/level also.
Bestial Roar should probably have it's save be 10+Half Level+Wisdom modifier instead of being based on the skill check. With the skill based systems (this and spellcasting) I'm working on, the DCs will be based off of the skill checks. I'll probably leave this as is. I still kind of question the large amount of points needed to gain the better effects, but having a fear effect option is nice. This does need a duration on how long the fear lasts and you should probably change "Intelligent creatures" to either "any creature with an Intelligence score" or "any creature with an Intelligence score of 3 or greater." Duration was listed at 1 minute per level. I did make the language change, thanks.
Ferocity is like a more limited Die Hard. It may be passable if you can continue functioning even passed -10 HP, but with restrictions akin to the Rage Claws soulmeld on just how far down you can go. There is no limit on how low you can go. With Diehard, you take damage after completing a strenuous activity (like trying to kill someone). This allows you to fight almost unrestricted (offensive actions only).
Improved Grab/Trip are both solid, as Int feels like one massive dump stat here. I approve! Can't dump too much, or you won't get all the skill points you need
Natural Weapon looks like a solid ability, but you may want to apply the same restrictions on when you can retake it that you did with a few of the other abilities. It is listed in the beginning of the description "a total of 6 6 times, starting at 4th level, and you must wait at least 3 levels between selections. Also, you can go ahead and drop "instant" from this sentence "You may manifest all of your natural weapons with the same instant action." Other than that, I would suggest having the first time you take this ability make all of your natural attacks, current and future, magical. Not necessarily give them a bonus a la magic fang, just magical. Otherwise, DR may hurt. I may just add magical strike as a free granted ability at 4th level.
Pounce looks fine, just change the language to say "You gain the pounce ability" and your golden. Done.
Shocking should probably either be a lower action or last longer than just one use, kind of like what I suggested for venom. Changed to a swift action.
Speak with Animals feels like another filler ability, but, hey, now you know how Comrade Bear really feels about the rest of the party. again, it fits the flavor of the class.
Close Wounds looks a little underwhelming, but it does lead into more. Off hand, I'm not sure if anything out in 3.5 other than Regeneration can switch lethal damage to nonlethal. I may end up changing this to Fast Healing, but I don't know if that will make it too powerful.
Trackless Step is just another copied ability. Not much to say here Again, Ranger and Druid get it, and it fits the flavor of the class.
Woo! I loves me some Evasion. 6th level feels a little late, but, hey, you're getting it before the Ranger!
See some my comments on "Lesser Scent." Really, though, Scent can be a first level ability, considering ToB. see my comments on lesser scent. I'll think about increasing lesser scent to scent, and reducing the level of the rest of the chain. You may want to switch this to limited blindsense.
Aquatic Adaption should probably just give water breathing. If you just want it to give Hold Breath, click here for its normal wording. Added hold breath under Swim like a Fish.
Beast Form looks fine. I'm inclined to increase the options to "any medium or smaller animal form, chosen when this ability is activated." A bit of a can of worms, but certainly better than Polymorph. cleaned up the language on all three.
Ooooh, I like Circle the Herd. However, I would either remove the DC 21 to it and make it just opposed by Sense Motive or vice versa. Giving people attacks is nice, even if they are techincally AoOs. Done (DC check only). Also changed it to a Move action.
For Larger than Life, I'd go ahead and just make it an actual size increase, rather than giving Powerful Build Lite. Wizards have had Enlarge Person for ages now, so why don't you? A good point. Also done.
For Rend, the damage is usually 2x base claw damage +1(Maybe 1.5x?)Str mod. Also, it should be "2 or more claw attacks" for those out there for more than the usual amount of arms. Done (kept the x2 Strength mod, though).
Spines looks okay. The bonus to natural armor feels a little weird, but it's not a bad thing. I would also allow an option to shoot the spines as ranged attacks, but only every other round, as the spines "regrow." If you go that route, maybe even through on a bigger attack with them, but at the cost of losing the benefit for a little while (1d4 rounds). I copied the language from a potion in the MiC. I'm not sure about adding the whole "shoot-the-spines" thing, but I'll think on it. Really, not many animals have a ranged attack...
Sprint is a little underwhelming to me. Feels like filler. Not sure what to do with it, though. With some decent ranged options, it does open the option to kite enemies. It can function like Expiditious Retreat for the discovered scout, and it makes it easier to close on an enemy. Maybe I should add something about getting a bonus to avoid aoo for moving through threatened squares? or decrease the level (and check/cost accordingly)?
Wolf Pack Tactics looks nice. I'd maybe have it progress such that "Any allies that also threaten the same enemies as you are treated as flanking for all purposes. If they would normally be flanking with you without including the benefits of this ability, increase their to-hit bonus from flanking by +2." Maybe also decrease time needed for the AoO option. Updated. also dropped the action to Move action.
I'm inclined to make Flight a 24-hour ability, with or without making it (Su) in nature. Warlocks have Fell Flight, so why not help the Beast Warrior save on points. I've increased the duration to 1 hour/level.
I'd go ahead and just copypasta the language from Claw of the Warrior. That would help out slightly with the language, but, if you want it as is, it would mean having three attacks at X, X-5 and X-5 rather than X, X-5, and X-10. I'm not sure which would be better, as one option would let you have more attacks sooner, while the other offers the secondary attacks a greater chance of landing. I'm more inclined to the former, considering the second time you would take this ability is at 20th. I don't know. I'll think on that one further.
If you take my suggestions for Lesser Scent, Scent, then I would either make Blindsense Blindsight or just make this Blindsense last 24 hours instead. I'm considering reworking this tree. See scent.
Commune with Nature is an okay spell, but it's primary users have had it for five levels now, which is kind of sad here. Not sure what else could go here in addition to it or instead. The Ranger doesn't get access to it until 14th level. I didn't think Druids got it -- I was mistaken, and they've had it since 9th level...I'll think on it.
I'd just change Improved Extra Natural attack to granting Multiattack instead. Hell, on top of that, I'd also either decease the level of it or also have it give Improved Multiattack (No penalty for using multiple natural attacks, but I think it's a little tricky to qualify for.) You may want it to only give Improved Multiattack if the Beast Warrior already has Multiattack, though. *shrug* I may change that. I've already changed the wording to add in the multiattack features, but I may just change it to multiattack.
Like what I said on Blindsense and the rest of that chain. Although, this may be fine eating up points to activate. See my other comments on this tree.
Eeech. Later HiPS is very late. I'd bump this forward several levels. I've added it under the Hide from Notice ability (after they reach a +10 bonus).
Fast Healing feels a little late to the party. Yeah. I may be upgrading the tree to give Fast Healing later, but it makes me nervous about possibly overpowering things. I'll probably change this to Regeneration, eventually.
Greater Extra Natural Attack is basically Improved Multiattack, but only at 20th level. Yeah. See my comments on ENA. I'm not sure what to place here instead, if I change things.
Supreme Savagery feels a little underwhelming by this point. I would probably increase the base extra damage to +4d10, maybe even +6d10.
Added "for each natural attack this round" like with the other 2 in the tree.
Overall, the class doesn't seem like it can actually provide in the skirmisher role, like you suggest: it just doesn't have anything to do at range. Very few animals have a ranged attack (except like the spitting cobra and such). What if I give them access to bows? The higher level abilities seem a little lacking in number, but that's understandable for a work in progress. I would also go ahead and include a general option for all abilities with an activation of "one standard action" to become swift actions, either as a feat or as extra BP, like some already are. I already changed some, but I may add a feat like that for the rest.
Other than that looks good so far. It's a little weaker than the Psychic Warrior, due to the issue at lower levels with the skill checks and the low amount of options at higher levels. Still, not bad for a first (or is it second) draft. Thanks.