Main thing I want is better controls -- WASD to pan the camera, Q/E to rotate, and ideally keyboard shortcuts for actions / buildings.
(Thankfully this is possible by patching the engine (and I did for WASD), it's just annoying to do.)
Secondarily would be fixing the rendering engine (culling and transparency is bad) and adding better graphical effects.
Thirdly would be nicer rock presentation -- either with the higher-LOD promeshes, or even better by procedurally tessellating them. Bonus points for a project with better textures and bump/parallax mapping.
Oh, and a better FPS mode, with adjustable FoV and the ability to do anything normal raiders do, as you can in Dungeon Keeper.