Half-Life and Deus Ex use two very different methods of story telling, so I see where you're coming from. I, too, prefer Deus Ex, but I enjoyed Half-Life for what it was. Deus Ex actually had you making choices, and your character has a speaking role. Half-Life lacks these elements, the only choice being whether you want to see the ending or get a game over.
I find it interesting that the Half-Life style of storytelling is more popular. It doesn't require any thought on your part, leaving you feeling like an observer rather than an actor. There really hasn't been anything else like Deus Ex, but you see Half-Life's influence in a ton of shooters today.