FT Ghost is basically the FT7 Pro, changes from the FT6 Pro to FT7 Pro are mostly in the blade. Softened the blade, made some minor adjustments to the kick point, other minor changes too. If you like the FT6 Pro but wanted something a little more tuned, the FT Ghost is a good option.
Proto is basically a updated version of the Nexus 2N Pro XL (extra light) version. They got rid of the 5 sided shaft, sticking with a more traditional Nexus shape. Updated the carbon, carbon layering, stiffened the blade, added boron, and a few other changes. Lots of updates and modifications to an already good stick.
I personally prefer a softer blade, so the FT Ghost is more desirable to me. The Proto was very good though, but the stiff blade was not my personal favorite. If the Proto could be made with a slightly softer blade it would have been a very difficult time for me to decide between the two of forced.