I would like to see it on the source engine or the cry engine, but it almost certainly will be done on the Doom 3 engine. Oh well, real time lighting along with lightsabers will look very cool anyway.
Assuming they make a JK4 of course.
I would just love to see all the physics interaction with force powers in the source engine. Although I hear Doom 3 has physics, I have a feeling they will not be quite as big a part of the game as in HL2.
I would love to see a new combat system, one where you can control exactly where the saber goes (using inverse kinematics). Think about how cool that would be, REAL parrying!