The only distribution of Linux I've used is 12.10 (and now 13.04). I use the Cinnamon desktop, and it seems great, I've had no problems with it. So now I'm wondering, could you explain a little bit what I'm missing out on?

Its been a while since I configure my CPU, but I am currently running Ubuntu 12.10 (upgraded incrementally from 10.04), with an alternate desktop (Awesome). I have never* noticed a program not work because off this, including the applet icons. The main point to consider in this is that most of the programs that Ubuntu runs are not written, nor maintained, for Ubuntu. Therefore, they should work perfectly well with other desktops. The only incompatibility that Unity introduces is when you are actually using Unity. When you are using another desktop, a program that works in another distro should work just as well. If you install, for example, the package "mate-session-manager", you will install a traditional desktop, and still be running Ubuntu. There are many other desktops to choice from in the Ubuntu repositories. Admittadly, installing one not in the repos will be more complicated.

* I have actually run into 1 problem (with java) arising from the fact that Awesome is a non-re-parenting WM. This rarely came up, and was solved by claiming to be running 'LG3D' as my window manager, as that is on java's hard coded list on non-re-parenting WM`s.