MW3 - Pick up and easily play. No team work required. All about K/D for 99% of people. Small maps. Very fast paced, run and gun.
BF3 - Teamwork is the #1 thing. Winning and helping the team is more important than K/D. Large scale maps. Vehicles involved. Much more tactical, not your Rambo style run around like a headless chicken.
Very different games. I own both. I love the teamwork aspect of BF3, but a lot of my friends play COD and sometimes I just like to pick up and play for a few minutes. I personally like BF3 better, but it's all about your preferred style of shooter.