I'm going to conclude, since no one objected, that everything that tyroclix posted is correct. Right?

Now, if Johnny Alpha declares 2000AD on Kabuki, he's stuck on Kabuki the whole game. If Cosmic Boy (on the same team as Alpha) chooses to copy 2000AD for a certain action, he gets +1 against Kabuki only. He can't change or declare a different target for 2000AD every time he copies 2000AD right? (under current rules)

correct...

My suggestion: colored cross-hair tokens. maybe with a -> X and X -> symbol on it. So like the archvillian base color the guy with the red X -> token gets a +1 attack against the guy with the red -> X token.

If anyone decides to sell such tokens, just credit me and we'll be cool.

Now for the 300 pt game, it wasn't too hard to remember who was against who, but then again, I didn't have any wildcards, just the three Ultimate X-men figs.

Why is this? for the 2000ad we have been told that if your 2000ad figures is mc'ed and chooses one of your figs (cause at this point they are on the other team), that when the action is over and they return to your team that you are not stuck with what they choose and declare another fig as the target of the 2000ad ability, are they now going to change that as well or is the wording of the UXTA different in such a way that it will allow this.

It has to do with the wording of the team ability:
The keys are At Any Time During the Game, which means when your opponent MC's him, and Once This Choice is Made, It may Not Be Changed Back. So by definition of the power, because it is figure specific once it is chosen your done.

Unlike the 2000AD ability:
For 2000 AD all 2000 AD on your team get the bonus. So MC a 2000 AD and declaring a target to apply the bonus to effects only Your Team not the original owner of the 2000 AD.