1. I got to know the characters better on The Pacific. By narrowing the focus down to 3 guys and those around them, I felt more connected.
2. BoB I couldn't keep track of who was who. So many people and each episode focused on different people, so there wasn't as much continuity.
3. Less tangents. The Pacific stayed focused on a more compact story. BoB had 2-3 episodes that didn't flow as well with the main story. Particularly the last episode.
4. The battles were better designed. I realize that there was more action with The Pacific, but BoB's battles didn't always make sense. Whether that was cinematography or editing, I don't know, but I seemed to know better what was going on with Pacific.
5. The Pacific's two sex scenes were far more tasteful than the one BoB throws at you in the last episode. None of them were necessary, but BoB just smacks you in the face with that scene. Probably the lamest reason on my list.
If I had to pick between the two which I wanted to watch, I'd pick Pacific.