I currently have a N2 setup. Pioneer broke my head unit when i sent it in for my flex cable upgrade, and wont fix the problem, so I am gonna buy a new deck. But i was thinking, is there any difference or benefit to just upgrading the headunit, or is the brain the real piece that has to be changed to upgrade? also, what are the benefits to the upgrade from the N2 to the N3?

Well first off, upgrading just the display (n2-n3) won't change anything other than the fact that the bypass is easier to do with the n3, you probably won't have a problem with the flex cable in an n3, and you'll most likely have the most recent software(70mtp). Upgrading the brain (n2-n3) though will give you mainly two features that are definitely sweat. With the n3 brain you will have an enhanced ipod interface and enhanced sirius interface.

Personally I would only go with the n3 if you were getting it for a really good price, other than that i would just shell out a little more for an n4. Which is basically all the same as an n3 except newer maps, 7" screen, and bluetooth compatible.