No offense to the X books, but I've always thought the Avengers SHOULD be the center piece of the MU. The Avengers Big 3 should be the MU big 3 at least storywise (even if guys like Spidey and Logan are still the mega superstars in terms of popularity).
And Bendis in a weird way made that happen. By disassembling the Avengers, he made them the top franchise. By ripping the Big 3 apart, me actually made that trinity more significant. Cap, Thor, and Tony standing side by side once upon a time was no big deal... now it's an event of importance.
If all this remains in place, even long after Bendis is gone, then I think he'll have forged a pretty descent legacy.