I'm impartial when it comes to these 2 games as I enjoy both of them.
PES: I've always loved their attention to detail when it comes to creating an atmosphere for the game, things like camera angles, stadiums, even actually making an effort with the fans' graphic detail (see FIFA's fans to understand I mean). Their gameplay is fun, the team AI feels a little bit better than FIFA's team AI as they aren't opposed to creating unorthodox openings, the addition of off the ball control made that game that little bit more technical (which is good if you love a challenge). Graphics? Attention to detail is their thing, even the textures. My issue lies with the player movement and collision animations. The keepers also have this issue of parrying the ball more often than they should.
FIFA: What they have always payed attention to is user gameplay, the player movements feel authentic, the addition of their collision engine did wonders (with the odd slip up

), the unique referee personalities is a nice addition. They've definitely got the better commentary IMO. Those unique traits on some of the players stats really come into play during a match. Graphics? They've improved over the years and some may even say they've caught up to PES. My issue here lies with team AI, it always feels a bit rigid regardless of whether or not you tinker with some of formation settings, then there's the fluidity of the tricks you can perform.
My history:
2010: I enjoyed PES more
2011: I enjoyed playing both equally for different reasons
2012: I enjoyed FIFA more
In any case there's a lot that I can say for both franchises, both are great games. I've yet to try the demos for their '13 installments. It will be awesome to see how these 2 clash. I will most likely buy both (PC).
Disclaimer: These are the ramblings (opinions if you will) of an ordinary man. Take it as you will.