I agree with John Gruber that "There are no absolutes in either (Web vs. Naive) of these arguments.", but there's one point in his argument that is overstated.
But app stores are mostly only a pain in the ass for developers, not users. Installing and especially updating apps through app stores is obvious and easy for all of the modern mobile platforms.
App updating is easy, but it occurs way too often and is dependent upon a good connection. On average, I have to update 3 apps per week. Often I'm on the train from NJ to NYC which has a spotty connection at best. By the time I get to the office I forget and the updates start piling up week after week. I wish there was a Google Chrome like model that just updated the app in the background.
Someone please release me from the red circle hell!