There are the generic aspects that befall any crossover: plot, power levels, antagonists, "If you give Bilbo a light saber, you have to give Sauron the Death Star,"; things like that.
Then there are the more specific aspects, like the interactions of the various power systems, whether one is just a different interpretation of another or if they're completely different, how a specialist in one handles a specialist in the other, are there any specific combination results, how will a generalist in both fare against a specialist, etc.
Then there are the characters. Are you meshing the characters? Importing them? Keeping the characters themselves to one or the other only (except perhaps for the protagonist whom you've already said is the new incarnation of the dude whose name I'm blanking.
Lastly, is keeping the focus narrow enough so that you can concentrate on one storyline without overwhelming yourself and the reader with too many details that don't interrelate.
Then there are the more specific aspects, like the interactions of the various power systems, whether one is just a different interpretation of another or if they're completely different, how a specialist in one handles a specialist in the other, are there any specific combination results, how will a generalist in both fare against a specialist, etc.
Then there are the characters. Are you meshing the characters? Importing them? Keeping the characters themselves to one or the other only (except perhaps for the protagonist whom you've already said is the new incarnation of the dude whose name I'm blanking.
Lastly, is keeping the focus narrow enough so that you can concentrate on one storyline without overwhelming yourself and the reader with too many details that don't interrelate.