Personally, I would like to see a darker Age of Apocalypse version of the members of the Great Lakes Initiative. It only seems logical for them to be present.
- They're mutants, so that gives them a good reason to be mentionable in a mutant-ruled reality.
- They're underrated, namely in that they each have potential as characters if they could move past their silliness.
Mr. Immortal should definitely have an advantage in the AoA "survival of the fittest" world (he's at least a survivor).
Doorman is a living portal and could therefore use his powers much like Kitty Pryde to avoid attacks.
Flatman is a lot like Mr. Fantastic and could certainly be a threat if he was a slightly more serious character.
Big Bertha is basically like the Blob, except that she can also shrink back down - and Blob already did quite infamously in AoA.
Finally, Squirrel Girl is already uncannily amazing in mainstream continuity, so a more brutal version would probably bring her up to Wolverine or Sabretooth levels!
It just seems like a wasted opportunity if none of these characters get some interesting alternate counterparts, and the AoA reality/comic series seems like a great place for them currently.