The problem is that monodevelop has a lot of dependencies that you will need to install manually (as in, without packages, like you did with Mono), such as:
- gtk-sharp (the 2-12 branch)
- gnome-sharp
- mono-addins
And some other that maybe I'm forgetting.
If you really want to live on the edge but without suffering so much pain, you should, first, stop using a LTS distro (install 12.10 for example), and then grab preview mono 3.0 packages from here: http://www.meebey.net/posts/mono_3.0_preview_debian_ubuntu_packages/
This way you will still be able to use the packaging system for installing dependencies like the ones listed above, and then you can clone monodevelop from github and use the latest version without problems.
Another option, in case you don't want to upgrade your distro, is that you install mono 3.0 in parallel with the mono 2.x that comes with the distro. To be able to do this you need to have special care: have a good read of this guide.