The average Linux application can barely manage to provide a tarball and an Ubuntu/Debian .deb (which will only work on a few recent versions of Ubuntu). This leaves other distros out in the cold, and even slightly older Ubuntu versions can't easily get many apps.
Desktop Linux doesn't need radical innovations. It just needs a stable core and ABI that doesn't change for 5-10 years (like Windows XP) where you can install any application on "Linux Platform 1".
I'm on the cusp of uninstalling desktop Linux having used it as my main desktop for about 5 years now, and after a decade plus of using Linux generally. Mostly because I'm past the phase when spending a lot of time on getting Linux to work was fun, and I just want my desktop PC to work, with all the hardware enabled, no sound problems, no full screen Flash requiring a reboot, no frequent Firefox hangs for 30 sec, etc.
I will still keep Linux for web software development in a VM, but for that I only need a server distro, where Linux is currently much better suited. I will also use desktop Linux for an elderly relative where it has all the applications needed, mostly, and for servers.
It's a great shame - Windows is as prone to viruses as ever since nobody keeps their third party apps up to date. I've had three mass emails recently from Windows trojans, including one from a techie with up to date antivirus. So there is definitely a niche for Linux as something that's more secure than Windows, but supports third party hardware unlike OS X.
One problem with the stable core + app store model for Linux is security updates - without something like Secunia PSI (a free vulnerability alerts and updates tool that's only possible due to funded high-end vulnerability management tools), it could be more painful to ensure that security related updates are done. If the app store tool only does 'update all apps', some vendors will end up taking features away after you have paid for them (infrequent but has happened on the iOS app store).