I've thought about this a bit. First off, I would get rid of the non-useful vehicles (GUN Car, for one), but keep some essential ones (like the parachute rocket).
I'd also make it so for any given mission, there are at least 5% more objective items in the level than you need to complete the objective. Some stages did this, but others did not.
I'd have Studio Blur, the ones behind the CGI cutscenes for the original, have exclusive cutscenes for pure evil and pure hero endings.
A firefight mode of sorts to see how many enemies you can defeat in one life.
Make chaos control be a slowdown ability than a warp one.
Minimize story contradictions that may occur through the branching and weaving paths.
Those are off the top of my head.