I guess I've kind of put Master League behind me with the new Become a Legend mode available. It's far more rewarding to play PES that way than it is in the Master League, though I know a lot of people want to do all that team management, etc.
I really haven't found the off the ball team movement to be as bad as you say. Players are usually in the right position to make runs. Once again, BaL really shows off the spacing that players try to maintain and you can really set up some nice stuff if you're playing in the midfield. Also, maybe try changing the difficulty a little bit? I've noticed the game plays a lot differently depending on the choice you make there.
As for referees calling fouls on legitimate tackles... have you ever coached a team? They do that all the time. Drives me nuts when I'm on the sideline.
Finally, as good as I think the 360/PS3/PSP games are this time around, the Wii version of 2008 is the definitive one. It completely changes the face of the series and soccer videogames in general, mostly for the better.