This is kind of a prediction, since at the time I’m writing this, Papers 2.0 is not out yet. But I think it all boils down to the 30% cut they would have to give to Apple.
The advantages of the Mac Apple Store are basically two: visibility and simplicity (to install, pay and upgrade). The disadvantages are that every upgrade has to be review and accepted, and that you lose 30% (well, probably slightly less, since every payment system will cost you something).
But Papers.app does not need visibility: it’s already well-known in academia, an environment where collaboration and information sharing (including the software used to get things done) is broadly practiced.
And Papers users are usually geek enough to not notice the easiness of the Mac App Store anyway. At least I know I am :)