Faces/Player Models - As a FIFA fan (see post above), I do agree that this is the one area where PES had an advantage, at least with the few star players that a casual soccer fan may recognize. However, FIFA 11 made big strides over FIFA 10 (IMO) in this regard.
And while the player models might have been better, Konami has always had a problem with the rest of their visuals, particularly the texture of the grass. Yuck.
Master League - I'm not going to pretend that FIFA has a perfect career mode because anybody who played FIFA 10 knows that it was a glitchfest full of broken promise. But I did still
play it. And Master League, at least in every version I've seen it in to-date, is marred by that Konami/Japanese style where it looks like it meant for a computer programmer/engineer instead of a video gamer. The features (particularly the new online mode) look great on paper, but I think the layouts, interfacing, and strange decisions (like not using real currency) scare off 80% of the would-be users.