Before 2007, I'll say PES had the upper hand with its features and most importantly, game style being more realistic.
This considerably changed ever since. FIFA improves its gameplay each year till the latest being a real realistic jewel if compared to the real-life matches. The AI level increased considerably and by all means, it shove down PES 12. PES still hasn't improved as much compared to its previous years. The only thing still maintaining PES as a proper game franchise rival to FIFA is the Official License given UEFA for Champions League features. The day, FIFA gets the license too, I think PES will be as good as a shelved or as a third-class game.
So, by all means, FIFA 12 is much much better than PES 12. If you just want more ideas or more specific details as to why FIFA 12 is better; just compare the Ratings and Reviews of the two games.