My experience with both games goes like this...
I first played FIFA 2000-04 with out rivalry and got more and more depressed - I mean, to be fair, remember those unstoppable spin moves? I used David Seaman (!) to spin 23 times (count them!) and score past Schmeichel in 2001... My main hate with the FIFA games was lack of change...
Introduced to Pro Evo and was blown away - I never won 10-2, stars did what stars do - it was a game of football that needed more than a memory of when to pass the ball...
FIFA however has re-claimed me, and PES is now the franchise resting on it's laurels - I love both franchises, and this ebb and flow is going to force the games to continue improvement...