The gameplay is much better than FIFA IMO, it's also better tactically, you can see your opponents exact formation and individual player stats, which helps when coming up against a relatively unknown side.
Also, any player can man mark any other player, which again, is a nice touch tactically, full backs staying with wide players, DM's snuffing out AM's, your wide players running back with their attacking full-backs, that sort of thing.
The Master League is a shambles though, FIFA's Career Mode is much more realistic in terms of dealing with the press, players, club hierarchy, your results actually affect your job status which brings a bit more excitement to the next game.
With PES's Master League I just feel like I'm going through the motions a bit.