Not much. The challenge always has been understanding the assets to a level nobody else has managed before. With modern tools and middleware, you could hammer out a greenfield Jedi Knight clone in a couple of weeks (not including content), but this isn't greenfield.
For example, keys encode mesh rotations as pitch-yaw-roll and with derivatives. iow, JK animations use Euler angles and mandate linear interpolation tweening. Spherical linear interpolation between keyframes does not work, I tried, and frankly I expect there to be at least one animation in JK that depends upon gimbal lock anyway. There is no modern animation package or technique which can be meaningfully applied to what JK is doing.
A lot. It was supposed to have drivable vehicles, at least. There were at least two levels cut late in development: level 5 (which was supposed to have a swoop gang), and level 13. Robert Huebner's GDmag post-mortem talked about how 04escapehouse's water tower puzzle was hacked together, and they were all impressed and surprised at how creative the level artists got with COG. I guess it was a different time, but it seems like the developers spent most of their time dicking around instead of working toward a real design.