The mod community is one of the last fortresses of old-school gaming genius and creative freedom left on today's scene. It really harks back to the glory days of young PC gaming, back when, you know, map packs were given away for free.
Part of what is so frustrating about CM is the fact that they have so many good elements. The weapons are fine (though not perfect) sounds, music, even the models and levels are tolerable. It's almost like they just nerfed the presentation worse than everything else.
I think, given these same assets with a devoted team of programmers without their heads up their asses, it would be easy to craft a few levels or even a small campaign that is much closer to Aliens than the end product.
I mean shit, many people have already said the core things: remove or edit the goddamned horrible AI buddies, cut the WY idiots waaaay down (if you leave them in at all) and give the Lurker AI to the standard warrior. Those are just a few easy steps that would drastically change the flow, feel, and gameplay of the game.
Everything else is all frosting, and besides the graphics, it's mostly fine. It's the cake that sucks so hard.