Lack of backwards accessory compatibility—even if adapters are available—is a problem.
And one that’s going to happen someday anyway—we can’t expect the same connector forever. That connector has been around since April 2003... nine years!
So whatever replaces it (to last another 9 years I hope)... small is good!
FWIW, I thought I read somewhere that Thunderbolt is not currently possible on iPad/iPhone because of the lack of PCI Express architecture. Don’t quote me...
Still, Thunderbolt can adapt to many purposes, and Apple might offer dock cables with Thunderbolt on the computer end. (I don’t see that being standard, though: USB will remain the standard bundled cable-end for now because everyone has it.) Anyway, while Thunderbolt speed would be nice for especially large syncs/restores, I find that in more ordinary use syncs are smaller, and therefore pretty fast (after iOS 5 especially) over USB. And of course it can all be wireless now.