There are three big problems I've noticed two stated by the original poster:
1. Fragmentation. Do you release a tar.gz? Do you release an RPM? Do you Release a .deb?
And how do you support them all? What really should happen is one of two things. 1 Package manager for all distros.(Not going to happen any time soon). The other is a 2nd compatable package management system which is compatible/an add-on to the existing Package Management systems. This way as a corparate developer I can just make and maintain one package instead of three. List the library requirements and if your distro can't go up to the proper version you can try to force it (like if your distro back ports a feature/fix).
2.
Rabid hatred of DRM. You know what though I would love to be able to watch Netflix on my Linux desktop so I don't have to fight with my roommates/watch the Jersey Shore marathon while waiting for the PS3.
3. GAMES GAMES GAMES:
Being able to play games native/ minimal emulation would be amazing. I know there is Wine and Cedega and CrossOffice, but they are just band aids to the real problem.