Well, fs2_open is the product of the Source Code Project and it contains many fixes, imporvements and general cool things
For one, most of the bugs that were in FS2 have been fixed. Some of the constraints that limited modders have been removed. And there are several cool new features which have been added, such as: Specularity map, glow maps, cloaking, DirectX8 support and others.
Most of these new features (not the fixes, the new stuff) are for the time being in their own seperate builds, though I imagine they will eventually be incorporated into a single exe..