The active abilities wouldn't be so overpowered that they would completely imbalance the game, they are only there to help create different play styles so each character feels different, moves different, combos differently, has different set ups for their signatures and so forth. After all not everyone gets to go SuperCena.
As we know everyone does crazy stuff in All Stars, so would Mick Foley, I did not consider daredevil dives as part of his ability because nearly everyone in All Stars already does them. When I think of Foley I think of the incredible amount of damage the man can take so I translated that into him taking less damage than everyone else. Is it an unfair advantage? Maybe. Is that how he really is though? Yep. Would that imbalance the game? Possibly, but if he were one of the slower characters with slower punch speed than the average Brawler would that even him up a bit?
But some of the temporary abilities work just as you described. For instance in an actual WWE match John Cena would only go SuperCena at a critical point in the match usually near the end, so in gameplay terms as you said you may have only 20 seconds in the match that you can use that ability, so you're gonna want to make it count. I have a different take on SuperCena mode though, I'll have to work on adding him in so everyone can see it.
Really do appreciate the feedback maskedmaniac, and interested to see what other ideas you or anyone else may have. I don't have every character laid out yet, and I may run out of ideas, so all input is good input.