See, here's the thing...the High Evolutionary *did* depower all the mutants.
All we got were some throwaway tales about the Neo (a more advanced mutant? seriously forgetting here), who had had some members die and they were upset about it. No X-Men died, no innocent bystander mutants living in Mutanttown...none of that. Well, Wolverine was suffering from andamantium poisoning.
So yeah, they probably didn't want to use him again. Plus they had to tie it to the Avengers somehow, for Bendis' status-quo shake-up.