I never finished F2, but I'm not sure you can compare it far with Deus Ex. The first is, like its predecessor, gritty post-apocalyptic but with a vaguely 50s retro feel and, as I said, a wicked sense of humour. You pretty much have the freedom to go where you want, when you want, and putz about on side quests.
Deus Ex is pretty much pure cyberpunk. It's at least as dark as Fallout but approaches it a different way- lurking conspiracies, everyone a pawn in an invisible game, atrocities and abominations wrought in secret by the hands of man, urban decay... with fallout, it's more slavery, drugs, and prostitution run rampant, horrific mutants, mad computers, and dangerous wastelands, hundreds of little factions squabbling over what resources remain while bigger fish plot to shape the future in their image.
... Okay, I guess there is some basis for comparison, just in different styles and settings. In one, you come from an illiterate village... in the other, you begin as a cutting edge new kind of government operative.
Being first person, Deus Ex doesn't provide such complete freedom, and the plot is more linear- but it's also big, and the plot gives you important choices and occasions where the later game is directly influenced by your decisions- without telling you "ok, choose A or B" but rather letting events unfold naturally. It's also notable for offering multiple solutions to any given problem. It's up to you whether to use stealth or brute force, and most obstacles can be circumvented for the right price, or if you're clever enough. You also have the option to use non-lethal force.
Oh. And Fallout 2, like Fallout, is a good game, whereas while Deus Ex is absolutely brilliant and I need to find a copy, Deus Ex 2 is a pile of crap that it's better to pretend never happened.