Neither.
International Superstar Soccer 1998 is still the best football game yet. By far.
I haven't bought a lot after that, as the ones I bought were horrid (and the ones I played at friends' places too).
PES has slowly become more and more Fifa. They've taken out the tactics, and made it less of an RTS, which is exactly what a football game really should be.
If I had to choose between PES and Fifa, PES wins by far. Still, it is nothing compared to ISS98.
Oh, and don't get me started on the later ISS games :(
http://www.vgchartz.com/games/userreviewdisp.php?id=261
That is VGChartz LONGEST review. And it's NOT Cute Kitten DS