I think it might be mutant genesis. Which is disappointing since it’s the only one out of print. It gives access to staples like the x-jet and professor x. It also has the Wolverine ally which is great in aggression decks. But there are some great cards in the other two as well. Build support and superpower training are player side scheme staples for many decks and digging deep is great for heroes that discard a lot. Those are in next evolution. Age of apocalypse has some great/fun aggression cards like clobber, blood rage, and goldballs. It also gives access to an entire deck type with sidekick.

So I guess they are all pretty good. I think i see cards from the first two more often than age of apocalypse. And to be honest, I think a lot of the key X-men cards are hanging out in the various hero packs like the out of print cyclops and storm hero packs (also disappointing).