Uh oh. Can I just say, while I love both SS2 and DE1, and they will forever be classics, it's not just the graphics that are dated. A lot of the mechanics are weak, and some systems are needlessly complicated (and btw, fixing these issues is not to be considered 'dumbing down'). I tend to play them both every few years, and always find interesting design elements, but there's also plenty there that dates them aside from the graphics.
Deus Ex especially was an important game, as at that time we all thought that games like that were going to be the future. In reality, they were the past. Modern design is all about taking a handful of strong mechanics, and refining them to the nth degree. Games like Deus Ex tried to do *everything*, and that in itself was exciting. It's this feeling of being able to do anything, being able to influence the story, being able to tackle things your way. That is Deus Ex. However, the mechanics that make up the Deus Ex or 1999 seen in the cold light of day are very weak by todays standards. For example, the stealth mechanics are pretty damn weak. Weak in terms of player feedback, weak in terms of feel, weak in terms of ruleset. It didn't matter then, we'd not really seen it done much better, and to be able to have that choice was novel.
SS2 has similar problems too. I love these games, but the world has changed, the audience has changed. You COULD NOT just re-release them with a graphical refresh and expect a fresh generation of players to have that same experience we did.
As a Game/Level designer by profession, when I'm working on levels and mechanics, I really don't care what it looks like until the very end. It's the final bit of polish to the experience. So far, I think the design of DE3 looks promising, and visually I think it's looks pretty distinct too. I remain cautiously optimistic . . .