The Mac App Store is off to a great start, but it's not all sweetness and light. Users have been confused by how some third party apps bought elsewhere show as "installed" in the store UI whilst others don't -- and in fairness, it is confusingly inconsistent. Meanwhile, developers are struggling to deal with the lack of upgrade pricing, and what that means for their existing customers.
As with the iOS App Store, everyone buying an app pays the same price, whether they are a new customer or someone who bought a previous version. There is also no ability to "grandfather in" licenses from elsewhere. For example, I purchased Pixelmator v1.6 from