Graphics: PES (Because they have more detail and better animations than FIFA's)
Players: FIFA & PES (It depends on some installments because there are some that are played with 2 or 4 players via Ad Hoc)
Deep Career: PES (For the Be a Legend Mode introduced in PES 2009)
Player Customization: FIFA & PES (Both have quite varied player customization system)
Controls: PES (Because it plays in a similar way as the Console versions)
Smoothness: FIFA & PES (Even though all their games run at a solid 30 FPS)
AI Intelligence: FIFA & PES (Although it may vary depending on the annual delivery and the difficulty you are playing)
Game Modes: FIFA & PES (Both have a variety of game modes and are distinct as well)