I've tried to stick with functionality that already exists in some form or another or is an extension of existing abilities. Disabling specific class functionality doesn't really exist in the game at the moment and wouldn't be useful in PvE (since said "special abilities" are intrinsic mechanics that can't be ignored) while being specifically disadvantageous to some classes more than others in PvP (imagine disabling survivability CDs, which would have negligible effect upon Sages since they have none, possibly excepting the new Force Barrier, while it would have a major effect upon Shadows, Guardians, and Sentinels), not to mention it's hard to define "special abilities" since it's not an explicit category of abilities (ex: is Defense Screen for Scoundrels in the same category of abilities as Saber Ward for Guardians?). As far as the game is, mechanically, concerned, there are only attacks (CCs are actually attacks that deal no damage), heals, and self buffs so, in order to do anything like you're suggesting, you'd have to either create an arbitrary list of abilities that would need to be kept absolutely up to date or go through the game and create separate categories of self buffs and attacks exclusively for that mechanic to be implemented. Either way, it's more work than it would honestly be worth since it would, functionally, be only useful for PvP against specific targets.
I didn't really have the patience/desire to search and research your post on the topic, so I won't comment on that what I did not quote.
As for disable, BW are doing that right now with Electro Net. Except it's selective disabling of mobility cooldowns.
And yes, I understand precisely what disabling everything but basic attack would mean. I play a healing Sage, among others. Not saying it's the way to go, and it can't be selective debilitation of, say, major offensive, or major defensive skills, but how's a short (2-3 sec) ability lockout worse than a hard stun (ignoring Resolve, of course)? So far disabling effects of Net can be overcome with the CC breaker, or, if I'm not mistaken, can be cleansed off, so I'd imagine this kind of utility would have a similar counter.
As for PvE, Obfuscate and smoke grenade don't apply to Ops bosses as well. So I don't see how something that's relatively useless in PvE can't be implemented as PvP utility.
Other than that, I'd love to see a "True Strike" mechanic which allows one specific, or a following attack to ignore all forms of mitigation and avoidance (other than raid encounters, naturally). Simply put, "Lol, you can't kill me while I'm getting healed to full" mechanics need a hard counter. WoW did well by making Paladin bubbles and Mage Ice Blocks removable by Warriors and Priests. I imagine Force Barrier would also meet rage and hate (probably to a lesser extent than Undying Rage but still).
End of mini-rant.
P.S. PBAoE pull is great. I've been pushing that for Defense Guards some time ago. Disengage, I'd rather give to Mercs/Mandos, since they have a jetpack already... from a "makes damn sense" point of view, rather than from game mechanics point of view.