Having played both on PC Fifa is miles ahead of PES for me, and contrary to what some are saying I'm loving the player individuality and especially weak foot simulation, I'm messing up loads of passes/crosses/shots because I'm trying to do things with the wrong player, trying to do things when not set in the right position or off balance, trying to do things with the player's weak foot etc. etc. And this is just in FUT SP mostly with Sheffield Wednesday players, can't wait to get my teeth into career mode with slider tweaks etc.
Certainly helps the visuals look like this:
But that's far from the primary deciding factor, I love the gameplay, smooth, responsive, varied, unlike PES in all its clunkiness.