Nah.... The differences are there in real life as well. What I suggest you do.. is find a team that you get used to, find your perfect tactics and stuff for that team. And I am sure you can take anyone on...regardless of teams (in 7/10 games that is)
I had a good roll with Ajax on PES 5 online. Rosales and Mitea as wingers and a goal hungry Babel on top was a fierce unstopable attack!
And no... I am not a Ajax fan.. The tactic I had just kicked ass