Nothing major, really. More like refinements and minor modernizations.
I would love to see grenades be affected by the game physics, such as jump pads. Low-gravity stuff could really make sense then as well (a'hem, Ziggurat Vertigo). Likwise, I always wished the larger projectiles (like rockets and grenades) could follow players through portals.
I never liked that the Lightning Gun doesn't discharge in water, either. Of course, I can at least get my fix of that with the Slipgaters here.
I do think that you guys changed the BFG for the better. The pain-particles really make the gun stand out as more than just a beefy plasma gun.