Honestly, it depends on what you are looking for. I love them both, but they are really different styles of games.
The best way to explain this is to use movies for example. I think everyone will admit that The Godfather is a rather good film, at least from a directorial and script point of view. And I think that many of us will admit we enjoyed the hell out of watching Commando. I doubt anyone could, with a straight face, say that Commando was a better movie. But, for a lot of people, it is a more enjoyable one.
Same thing with Deus Ex (although DE is at least a really fun game as well :p). There are few games that are better. But it might not be what you are looking for at this very moment.