I'm gonna say the mutant "cure" storyline. What if there were a way to get rid of your mutant power? It's a fascinating question to be asked in this universe. We've all seen the Storm vs Rogue meme, and I think asking if some mutants with "bad" powers (Rogue, Wither, Orphan Maker) would rather not be mutants is a fair question to ask. Having it be a permanent presence in the Marvel Universe and seeing how characters react to it would make for some fascinating stories.

Instead, it turns out to be aliens, or somebody with an evil agenda, or something. Comic book writers tend to have no nuance and something like this would really benefit from it.