Nothing in particular, except incredible facial animations (which are still some of the best today) and perhaps physics.
Though almost everything it did may have been done before, it did everything right. Rather than sticking to just one gimmick or one major redeeming factor to set it above other FPS games; it took everything good about FPS games, stuck it all together, polished it to a shine and as a result created what is still the best FPS game ever created (imo). Only then did they seem to concentrate on the gimmick (the gravity gun,) and even the gimmick was awesome.
Take any other shooter and its generally considered good because of one or two things... Crysis is considered good because its beautiful and because it has open ended ways of approaching your objectives. Gears of War is considered good because it made cover mechanics slick and intuitive. Halo is considered good because it has great multiplayer (apparently) and generally improved console FPS games as a whole. Call of Duty these days is considered good because it has a multiplayer leveling system to add a sense of progression to the multiplayer, and because the singleplayer campaigns have many action-packed set-pieces.
Now look at Half-Life 2 and all the things people regularly praise. Even ignoring the physics, animations, art design, and (at the time) impressive graphics... Smooth, ease-of-use movement that isn't bogged down by pretensions to realism and allows for quick and precise maneuvering reminiscent of 90s FPS games. A fairly large collection of weaponry spanning all the cliches but making them more intuitive than ever before, very balanced, fun and satisfying to use. An intentionally linear path allowing for progressive storytelling and keeping you on track to see all the magnificent set-pieces and making sure you don't miss anything important. The story itself is nothing amazing but the way the story is given to you is done better than any other game; no cutscenes, no breaks in the action, just a fluent and non-convoluted storyline that you experience every step of the way but is given to you subtly through dialogue and the environment; rocketing the immersion levels skywards. Interesting, relate-able, realistic and believable characters who are voiced exceptionally, and in later episodes have an emotional impact to those of us who pay attention enough to care... I could go on.
It may not have done anything particularly new, but everything it tried to do it did better than any other FPS. and I have yet to see an FPS that can beat it in any other areas than multiplayer (which I don't care about) and visuals.