Fun fact, I just finished playing Deus Ex again a couple days ago. It never uninstalled it. Although, I have it on an older desktop that I got in 04 and I haven't tested to see if it works on my new laptop, or if it suffers from Thief Syndrome and won't run, but hey!
Anyway, I can't say the graphics bother me. I mean, they're not great compared to today's effects, but graphics really aren't what make a game. That said, there are two things that do bother me about the game. First, fucking ladders. It's needlessly hard to climb and detach from them - to clarify, detach at the appropriate time and in a way that doesn't send you falling back down - sometimes. Second, the AI is legendarily thick. If an enemy sees you, you just have to go into another room and close the door and half the time he'll forget you were ever there. Fix those two problems, though, and I'll gladly describe Deus Ex as a perfect game.