PES has much more tactical depth and is much more realistic in terms of how moves are built in and around the box as well as the variety in the goals you see. The new engine should bring nice improvements, eagerly anticipating the demo.
FIFA is smoother visually (better animations), and the licenses are nice but the gameplay doesn't feel like football - the fundamentals are all wrong. It's OK for arcadey fun in short bursts, especially in multiplayer Clubs, but there's no substance/realism to the gameplay.
In gameplay the difference between PES and FIFA i like the difference between Battlefield and Call of Duty - CoD is so popular because it's easy to pick up and play, mindless "run 'n' gun" based on reactions and repeating set patterns of play wins the game... Battlefield requires more thought and analysis on the game situation as to how to adapt your approach to succeed, it's a tougher game to play but has much more depth...