I've played with around ideas on this and with some of the games that have just recently been released or are still being worked on, it's clear that a sequel to JA must have a new engine, whether it be from scratch or using an existing engine (HL2, Far Cry, Doom 3 are definite candidates).
If they do develop another sequel, I believe they will expand upon the "create a Jedi" theme for SP.
I think acrobatics like wall running, wall flipping, etc. should feel a lot more practical and useful as well as looking cool (read: Ninja Gaiden), of course that would entail practical level design to incorporate practical use of such acrobatics (JA's levels were better than JO, imo, but could have been better still).
I also think the saber swings and movemements could look better, maybe mixing in a sort of kendo style influence or something, but the staff and dual animatons look totally out of place and generally goofy looking, and those staff kicks look pretty horrible (sure wasn't Ray Park doing the motion capture), and I still puzzle about the terrible walking animation for staff/duals.
Ah well, I can always dream that someone will create a game of the year sequel to JKA.