You know, they could've saved everyone so much trouble by sending Peter and MJ back to Portland and saying Ben Reilly was the new Spider-Man. Hell, you could even have him take Peter Parker's place and work at the Bugle, calling himself Peter Parker. And it'd make sense, because why would Peter risk his life when he has a newly-recovered child to care for? Plus, it would get him out from under the microscope of being unmasked. Just do a little double Spider-Man action and people start to think Peter's unmasking was a hoax. Then you could portray Ben however you wanted and no one would care!
That's right, I'm actually yearning for the Clone Saga at this point.