The age old debate.
Personally, I grew up playing FIFA, then played the PES4 demo by accident one fine day and so far, FIFA hasn't matched the gameplay or even graphics of PES on the PC. I only play on the PC so thats how I will make my judgment of both games, I dont give a shit about console versions cos I don't own any.
Anyways, I have played PES 4,5,6 and 2009 demo so far and FIFA 2000/01/02/03/04/08 and 2009 demo.
I think that FIFA feels too mechanical and the transitions between animations are no where near smooth as PES which flows beautifully from one action to another. It feels natural and the ball physics/player movement is enjoyable rather than being uhhh 'jerky'. Thats the major difference between the two. You always hear people say about the 'feel' of PES and this is the reason for it, top draw smooth animations.
The areas where FIFA is way ahead is Audio, Licenses, Presentation and Online.
Playing on the PC, one can utilize the god sent program 'Kitserver' (created by juice/robbie) along with patches for kits,stadiums,balls,chants,music etc. Its football nirvana !! Of course, these are user created patches but they give PES what it lacks.
I personally enjoy the PES Master League more because of its sports rpg feel and simple navigation. And wanting to play the game also helps
The online component still bugs me as I do play FIFA 2008 but ONLY multiplayer once in a while. PES needs a lot of work ( maybe m wrong cos I haven't got PES 2009 yet ).
So until EA provides a close enough gameplay to PES or gives Seabass truckloads of money to never make a PES game, I am sticking to PES.