I wonder if MSFT will stop supporting SDK's that don't run through their store long term. At some point will you only be able to write things that run on Windows that go through the Windows store? It looks like Win RT is going to go that route. I think it will be hard for MSFT to totally shut that down on mainline Windows for a while, but longer term it might all look a lot like walled garden distribution across all Windows.
I imagine that MSFT will have some kind of enterprise program where you can run your own Windows Store Server to do enterprise deploys of Metro apps.
Either way, it looks like Linux might end up the one place where you can install and run your own software over the long haul.