With Deus Ex, I think one factor that really boosts it is that very few games previous to it focused nearly as much on experiencing a story while giving a first person player agency of any degree, and this is probably doubly true for the kind of audience that would find a first person real-time experience appealing, or at least I imagine the audiences for Fallout and Planescape: Torment and such, while overlapping some, weren't really quite the same audience as for Deus Ex, and stuff like Lucas Film's Maniac Mansion style games (puzzle narrative games?) are even further removed. While other games that are obviously similar in some ways, like Half Life, are much much more on rails in terms of both player experience and narrative compared to Deus Ex.

I think it's a great game, just like the X-Files was a great show, but also just like X-Files was not a perfect show. (Though I'm not sure there's a strict analog to the degree of unnecessary continuation X-Files has had.) By the standard of its time, just being first person and having varied endings, varied routes, and a lot of narrative support are all big winners for its time.