PES just feels like football, while FIFA feels so scripted.
Now that I finished my school day I can give you a real opinion
FIFA:
Pros: Lots of teams, Be a keeper, Being able to switch teams in manager mode, more licenses, better free kicks, better keepers, Slightly better online.
Cons: For a game that has so many licenses, Fifa should have Champions League. Also it is scripted, and just feels unnatural. Passes are almost fully automated. Not much editing is doable. No respect to fans(They don't really fix any problems by patches and such)
PES:
Pros: Uefa Champions League, Europa League, and Super Cup fully licensed. Much more natural passing and shooting. better tricks. Online has less cheaters. Overall gameplay just flows naturally like in real life. Konami care about the customers(Shown in how when they released a patch that by accident changed Ireland's team kit to another kit, they fixed it super quickly). PES is improving, while FIFA is going downhill. PES allows for complete freedom in editing.
Cons: Some glitches make the game less enjoyable, Keepers and defenders are sometimes STUPID. Otherwise a fine game.
This may be a bit biased, but I'd rather play PES 2010(Which I could edit all team kits to new ones and all players and such with ease) than FIFA 11.