I like it, but I automatically like all mega man mechanics.
Is it too risky to ever be used?: I wouldn't use it if I had a Witch move that made the character for me. Other than that, I'd go for it.
Is it too complicated? To me, yeah. I would remove the concept of getting/losing basic moves. For NPC's, I would say 'You get their custom move' (OF COURSE they have a custom move, hold on a second *writewritewrite*)
Is it too mechanical? Maybe!
Is changing another character's move too powerful? Yes, and that's okay.
Do I think this means you can lose basic moves? Maaaaybe. And that's too complicated and funky for me.
Is there a more elegant wording that leads to the same results? State that you swap moves that they don't have. That automatically disables basic moves, and also doubling up on moves which would be weird. Also, you want to avoid the term 'special move' because that is confused with the 'special', which is a sex move.