Another vote for Deus Ex. Changed my way of thinking about LIFE!
FEAR was fun, and very, very well done in my eyes, but not revolutionary. Only thing it took to a whole new level was level design/atmosphere. May have also been the first to use music and sound on player cue.
I'm not sure which one came out first, but HL and Deus Ex are the first games I ever saw where the story WAS the game (Shooting is fun, but anti-terrorist terrorists, way too bloody cool.).
I don't think HL2 was really revolutionary.
Crysis definitely isn't revolutionary...I don't know where you got that idea. Far Cry....had a big, open world (for the first half), but Deus Ex had some big levels, and multiple, specific ways you could accomplish your goals. The only thing the openness in Far Cry did was let you choose which direction to attack from (more or less).
So yeah, a definite vote for Deus Ex. Crazy story, multiple path level design, able to sneak, be silent, or go guns blazing. RPG elements with the experience & levelling up (Improving your pistol skill, hacking, etc.). I'm not sure if it's the first on many of these things, but being popular is a big thing when you're trying to change things or make an impact. (Unpopular games with a cool X system don't change much).