For me, the canon changes in 4e are both a positive and a negative. Some changes were obviously required - forex, the change to alignment forced some creatures to be rewritten storywise. Some changes were made to update the current flavor of the game. Some I like, some I dislike. Either way, as others have pointed out, if there is a cool idea, you are bound to focus your campaigns on that and tend to ignore the stuff you don't like. This is no different than any other version of D&D so the issues are the same with 4e as 3e or 2e, its just more glaring because its more in your face than in previous editions.
Now having said that, one thought I had, and maybe it really isn't feasible, but what if they released a setting book in the future that re-established old canon. Instead of a Dark Sun/Forgotten Realms Setting booksit was Greyhawk (or whatever other name you would use to descirbe the old canon). It seems to me this would be one of the best ways to interest players who have not made the jump to the new edition purely for story reasons. While 4e makes some fundamental changes to the game, you could still get pretty close, storywise to the older editions. I wonder how a product like this would do?