The reason I suggested letting it stack is specifically because, as things stand, the player will end up with just about all of them anyway. Having something you can actually build up is nice. I don't see a decently high AC bonus as being gamebreaking on a melee-heavy class with only light armor proficiency, especially since each one is a natural weapon pick you're putting off (presumably to pick up with monster levels.)The reason for the NA Anatomy once is that one guy in the playtesting version of the class did the Natural Armor for all of his Anatomies, and also became super-armored. The main reason for the Anatomies getting stopped at level 9 is that, if continued with the current bundle of options, everyone would just end up with all of the options, without any diversity. Maybe if I can ever think of some more, I might extend the progression of Unusual Anatomy. Also, Don't underestimate Aspect of the Odd, as it usually turns out to be pretty useful.
I assume you're talking about Create Spawn and Alternate Form (Humanoid)? Create Spawn is a gamebreaker, but it would make more sense just to ban Create Spawn from the available abilities.On the monster "levels", the reason I restricted the maximum levels because some of the monster classes with lower amounts of total levels could be used to make the Student of the Weird way more powerful than the other members of the party, or, more importantly, the monsters the party will be facing. This is seen in such examples as the Ghoul and Aranea classes. Both can be used quite lethally in combat, or even out of it.
Here's the thing about Alternate Form: with the way the class progresses, it's coming in at level 14 at the absolute earliest. This is a level when Summon Monster VII, Prismatic Spray, Reverse Gravity or Limited Wish is considered a level-appropriate ability. I am absolutely not saying that the Student Of The Weird should be getting Limited Wish at this level, let's get that out of the way. However, at that level forcing the character to reset to another progression and get first-level abilities as his ability for that level (1 point of heat damage! Detect Magic 1/day! WHOO) is a seriously raw deal.
The whole point of this class, as far as I can tell, is to go into the interesting and weird abilities monsters have. For the most part, the "half levels or level 4, whichever comes first" restriction prevents the player from getting the actual interesting abilities and restricts him to more natural attacks and first-level spell-likes with a very few exceptions.