1) Depending on the plane, you might get a metal support beam cutting into your storage space under the seat in front of you if you're on the aisle.

2) It's nice to be able to lean against the 'wall' if you're in a window seat.

3) If you're in an aisle seat, and you have your shoulder slightly into the aisle, you can get smacked by the carts that roll by.

4) Sitting in the window seat, you don't need to get up everytime someone needs to use the lav.