I mentioned endurance, simply because it fits the same sort of "naturally tough as nails" angle an above average constitution score would, except without weirdness-issues where if someone poisoned you, all of your abilities suddenly turned-off.
I understand. However...being poisoned resulting in you having a lot of your abilities turned off makes a lot of sense if you think about it . Hmm....that gives me an idea for a Kimimaro-based class....

Reading it was clunky. As 3.5 deals heavily in either squares or cubes of a certain distance (usually 5 ft. to a side), it's just easier to reference what's already there.
Well, there's also a lot of spheres in 3.5 . Divine spells, paladin auras, frightful presence, abjurations, spreads, emanations...the real problem with those is, as my first Stillsword draft showed, that spheres are kinda clunky when their size is relatively small (i.e under 30 feet).

The recharge time does help it from being truly spam-able, but the random HP can become annoying, especially with poor labeling. Using static HP makes it easier to predict, yes, but when you consider that it even just has Hardness, well, that could be enough, especially considering how objects take reduced damage from non-sonic attacks.
That's pretty convincing...meh, ok, I'll use averages.

Looking at the permeabilities, the reflex save for flying and falling creatures is clunky, considering the default is just to have flying creatures have their wings "lock" and glide or float, in the cases of magically flying monsters like beholders.
The thing with Kinetic Allowance is that the birds/other flying things fall without moving or thinking during the fall, so they are caught by surprise. It's not similar to the default because there's no other ability which works that way (stopping time for everything except gravity itself).

I see no reason why "Allow Swipes" to be just restricted to slashing damage. If it's a flavor thing, why not allow for piercing and "kinetic bombardment (read, bludgeoning damage).
The main idea is that the structure of the membrane is of a flowing semi-solid, through which very sharp things can pass without causing damage to the membrane itself. The reason why I'm allowing only melee weapons is that ranged weapons would simply timefreeze inside the Still Space without anything else to propel them (whereas melee weapons gain momentum from the hand of the user, which is experiencing time normally). As for why I didn't allow piercing damage, that was just an overlook, added now.

Incarceration needs some clean-up on the wording. I know it does something to [teleport] effects, but I can't parse what exactly.
Changed the wording. It should sound stupid, but also clearer now.

Cesation of Existence should say if things inside come back.
I usually assume that if an ability doesn't say something, that something is not intended to be said. But meh, added "and do not come back, save for the effects of Miracle, Wish and Reality Revision".

I just personally dislike abilities suddenly stopping previous strategies from working. With your cleric example, it's always an either-or-type of deal. It's a design choice, yes, but "losing" haste just bugs me.
What bugs me is how a person who denies the very concept of time would want to be hasted. But we'll have to agree to disagree on this.

Denying dexterity is useful for setting up other forms of attack, such as Sudden Strikes and Sneak Attack, more so if they benefit the whole party. The issue here is Standard Action attack versus Full-attack. Denying Dexterity could be useful, say, against a light armored opponent, but you could still be housing yourself by doing one attack versus whatever your full-attack gives instead.

My main issue is that the "no crit" bit feels unnecessary. There are other (Su)-based attacks. They do weird things, but they all allow for critical hits to happen. By the time this ability comes online, you've also already got a minimum of three attacks per round on a full-attack. Is it nice to have for when you only have a standard action? Yes, but it's unfortunate that it has more drawbacks than benefits.
Um...no, you got it wrong. Any. Normal. Attack. Can. Be. Substituted. With. A. Flashstrike. So if you have a BaB of 16, you can Flashstrike 4 times in the same turn.

It is basically just an either-or decision between "Do I want to deny dex?" and "Do I want a chance at critical?".

1. You're a time wizard who may or may not have allies. Having conflicting abilities on PCs can be annoying, either because the two players are doing the same thing or because one's shtick hurts the others.
True, but there is no conflict to speak about, because Ripple has NO NEGATIVE EFFECT on your allies. It simply gives a positive effect to your opponents.

2. Mention this in the rules text then! Examples are good for that. Say if it follows the Stillsword in question or if he drops it and it "sticks" to the ground.
I don't think you read the ability carefully. Direct quote: "in a 200 feet area around him". Around him.

3a. It's a Supernatural ability. Thus, I assume it takes a standard action to activate (or is "always on"), and this leads to issues with how long it lasts and how many uses/day I have.
Another case of not reading carefully. Direct quote: "This ability can be suppressed or activated by the use of a swift action.".

3b.I'm using "magic" as a catch all term here to ask about what happens if an enemy (or ally) using some random spell to do something. Generally, it's as simply as going "Wish, Miracle, and other (your choice, as the designer) 9th level and stronger spells are able to bypass this effect." Sometimes a lowly Dispel Magic can overcome the effect. Things like that.
Ripple does nothing more than offer concealment . Spells work exactly as they would work on targets with concealment on them. If a 9th level spell ignores concealment, it ignores Ripple, if it doesn't, it doesn't. Again, I usually assume that if an ability doesn't say something, that something is not intended to be said.

Also, for a fight, the difference between 10 minutes and forever can be the same thing: after all, being dead means not being able to use whatever it is got shut off. Having it function without a check also means it "just happens" with no chance to save against it or stop it. The standard is for most of these types of "dispels" to be as a caster level check, as if you were using some variety of Dispel Magic. If nothing else, it prevents weird cases were a plucky ~10th level character turns off the world-ending "epic" level artifact twice his cast level. Not saying treating it like Dispel Magic won't stop that from happening, just that it would make it less common.
AMF lasts 10 minutes PER level. That is all I have to say really.

Eh, it doesn't sit well with me. I'd like it if it at least had some sort of opposed level check or the like happen, rather than just be a "Nope, I'm better than you, so I freely turn off all of your stuff!"
Isn't that the definition of Improved Uncanny Dodge?