Zone of Alienation change huge amount of stuff. Visually stunning, last time only Crysis1 give me similiar impression. You die from 1-2 shots and your enemies too, no cheating accurate AI IIRC. Plus stuff like ammunition system, magazines in your backpack, managing ammunition and putting it on your belt like in Lost Alpha.
Shocker Mod is mostly about guns. Lot of them, detailed, animated(!) and fun to use. Plus some tweaks to game.
Return of Scar is new storyline, didn't tried it yet.
Sigerious Mod for SoC is not that great like for CoP but worth check.
AMK is legendary, included in many mods that required max. 1.0004 version of the game, hell for Steam users.
Valley of Whispers is another storyline in some canyon, two version - VoW alone or combined with other mods, I played propably one combined with Shocker Mod, good combo IIRC.
Doom's Mod Merge v4 Anon Edition is best freeplay mod, you can play as any faction (maybe except zombie and mutants).
EDIT
holy cow ST2+AA2 work so slow. I know my PC is not great but damn.
Need to disable that crappy effect, just as I expected it's used in shitty way. Making blur everything in not logic way. Pfff...