I'm with SoundOfTrees: playing with more than one Legacy (or Bunker now) is a variant. Obviously, I'm not recommending that anyone should play with a team of more than one, say, Wraith. All of her character cards have Maia Montgomery, and it's likely that their progression is the Wraith's life, like...
Wraith--->RC Wraith--->LS Wraith
But they're all still Maia Montgomery, so they can't (or at least shouldn't) be played together. You could make a case for LS Wraith to appear from time travel happenings, much like it seems Greatest Legacy should, but the fact is they're still Maia, so you can't have more than one of them in the same game.
However, if Greatest Legacy comes foward from the past and meets his son and granddaughter, then they're clearly different people. So I think it'd be fair to say they can be played all in the same game, because none of them are actually the same person, time travel or no.
With the issue of limited cards, I think it's fair to have more than one in play if only one is played by a different hero deck. And in order to have more than one of the same hero deck in play, the previously mentioned condition must be met.
To summarize: Even if it goes against official rules regarding limited cards, A variant can be played where more than one of the same hero deck can be in a game if each of the character cards that go with those decks are different people. So, these characters and their decks may be in the same game:
Finest Legacy, Youngest Legacy, Greatest Legacy
Indestructible Bunker, Engine of War Bunker
Visionary, Dark Visionary
I'm going to have to say, though, that Unity and Golem Unity shouldn't be played together, because they'd become far too powerful.