At this stage, even though I would rather buy most of my apps direct from developers, I'm often half-afraid to do that because of the inevitable "what happens when they shift to MAS-only" question arises.
It's already happened with 1Password, Coda 2, Pixelmator and a number of my other favorite Mac apps -- it's hard, as an end-user, to support the old regime when maintaining two separate software branches continues to be a PITA for developers.
And that's the real problem. Developers retain two branches because they want to offer customers options (as well as legacy support for regular pre-MAS releases), but most of the Mac developers who are both selling direct and in the MAS are seeing much more income from MAS. If forced to choose, I can't imagine a developer picking the option that gets in front of fewer customers.
Still, there are some very, very real concerns for Mac software due to the new Sandboxing rules. Fortunately, now that the deadline has passed, we'll actually get to see just how bad it is.