While I agree with everything else you said, this is just a cop-out

The two main things I'd like are liquids, and the fully deformable buildings thing, instead of just walking up to an enemy brain and shooting it, you could dig a tunnel below the brain room and cause it to all collapse in on its self, maybe if you dig a tunnel and set an explosive off under what you want to collapse, then it just falls to pieces after the bomb blows up. Maybe making diggers tunnel a bit less effectively to balance it?

Also, more working buildings like Thanatos' Fusion Reactor would be good, like a mineshaft that brings up gold to the surface for easier collection or something along those lines.

Some specialized actors would be nice as well, like clones that can only use certain types of weapons (They come with the actor when ordered) but are extremely good with them, like a pistol clone could be a crackshot with a pistol, AK47 specialist could reload faster and be more accurate, but other weapons aren't as useful in their hands. Maybe a mining clone with a gasmask, and adding in dangerous underground gases that could kill other things that go near them?

Edit: Also, multiplayer would rock and fix the frickin' slow motion, it just adds in lots of lag until the game is near-unplayable, not the nice, smooth B13 slow-mo. Also, some kind of melee weapon for all (Base, at least) actors would be good, in case their guns get blown up. By melee I mean fists, or some kind of indestructible knife.

No.

Agreed.

you mean like save states like in some emulators?

I would also like that once it loads it never has to load again unless you add a mod or delete it.

Then it wouldn't be possible to test mods, you would have to delete it every time to make it reload it.

Indeed. I don't know why Data removed the ability to reload mods without shutting off the game, it's a pain to the modders. I have to close and open the game every time I tweak a variable.