Lest we forget, Harry Osborn's being alive makes Liz Allen and Foggy Nelson look like adulterers.
...are we to assume that Wolverine and Daredevil's powers work on everyone else in the world except Spider-Man? Surely they'd be able to recognize him as Peter Parker. And what about SHIELD's psychics and spy satellites?
Has post-OMD Peter shown up at the Baxter Building yet? Because if so, isn't there a mandatory DNA scan set to make sure you're not a Skrull or Dire Wraith or something and match it against Reed's database?
All the other New Avengers know each other's identities. Why didn't Luke Cage beat Spider-Man into a coma before Secret Invasion? To suddenly forget who he is like that should set off some Skrully bells.
Did MJ and Aunt May live in Avengers Tower?
Does this retcon affect the dead? For instance, do George Stacy and Steve Rogers up in Heaven or wherever remember that Peter is Spider-Man? If they came back, what then?