Lol, yeah, 3D models in a 2D game just doesn't make much sense.
And the other things are hard enough that they're just not feasible. OP2 is modable, but only slightly more than any other program out there is. The levels use DLLs, so you can do anything that executable code can do, but the supplied interface to the game engine is fairly weak, so there isn't a whole lot you can really do through it. Making basic levels works, but anything beyond that tends to take a serious amount of work and knowledge to do. Getting new behavior or units requires understanding how the game engine works internally and hacking it, or overwriting memory you're normally not supposed to touch.
If you're looking for easy mods, then you can change the graphics (tilesets are easy, units graphics are much harder), change the music, play around with the .txt files such as stats for weapons, and the tech trees, design new maps (possibly with new tilesets), and make simple level DLLs. I can't think of anything outside of that which is fairly easy.