I think the fact that to make a purchase you basically wind up creating an account with each plugin or theme company is ironically, probably part of the problem. Having a centralized place to get the best plugins and themes is a great idea -- it really is -- but the whole reason to do that as opposed to just using it for discovery and then buying it directly from the other company, is the easiness of a single-user sign-on.

The Expression Engine community -- which admittedly basically 180-degrees different from the WordPress community in everything from licensing to attitude towards paying for plugins -- has a plugin repository known as Devot-ee (http://devot-ee.com/) how it works is that plugin developers give a cut of sales to the Devot-ee staff. As a result, some developers sell their plugins for less money on their own sites. Yes most developers I know still end up buying all their plugins through Devot-ee.

Why? Why would people be willing to pay more? Convenience. Not only can someone do one purchase for the plugins they need for a certain site, they can also transfer licenses directly from their dashboard. So if you're working on a client project and you know you need X number of plugins, you can purchase said plugins and then transfer them to the client. Support takes place from the vendors themselves. In this way, it's really no different than any other marketplace.

WP App Store could probably do well if they allowed for that sort of ability -- or if they were able to work on setting up special plugin bundles (like get Backup Buddy, Gravity Forms and a WooThemes theme for $X). But for me, I know I'd want a central way of managing my plugins and purchases without necessarily having to bother with creating an account and separate login for the plugin maker himself -- unless of course it's automated to the point that it can share login info a la OAuth.