Asking FPS vs. RTS in a message board for an RTS will probably give you a skewed result; guess which side it'll be skewed towards?
Anyway, I prefer FPS. Better storylines, more character interaction and development, and generally more vibrant worlds. While there are a few exceptions (such as World in Conflict), FPSs generally are more realistic and more story-based. Mind you, I'm not talking about generic games like (bracing for flame) Halo 3 or most COD games. I'm talking about games like Half-Life 2.
Not to mention the obvious aspect of immersion. With an FPS game, it feels like you are the character you're playing as, especially with controllers like the Novint Falcon. With an RTS you're just a floating camera in the sky.
Of course, I still enjoy RTSs. If it weren't for the performance problems I seem to experience with any large-scale RTS game, you can bet I'd be playing SupCom and SoaSE most of the time. Due to the aforementioned performance issue, however, I can play neither for more than an hour or two.