I agree with you about the ball physics, though I agree with others about the much greater variety in shots in FIFA. There's pros and cons with both. To each's own, but after enough time with PES I always get the sense that I've seen it all, so I'll take the variety of FIFA personally.
But I definitely still feel like PES has that old on the rails feeling. When I was playing tons of PES this year prior to FIFA's release, I remember thinking how at times it almost felt like a turn-based game, as I'd regularly have to wait for locked in animations to play out before I could do anything. And then while the ball physics looked sublime, it all had a self-determined feeling about it, where as FIFA feels far more alive with a greater sense of never knowing what can happen. Again, there's pros and cons to each approach, but personally I find PES's approach behind the times and limiting, though I think the result is slightly more polished than what you sometimes see out of FIFA.
With fouls, yes PES has fouls called but FIFA is overall better with its physical interactions and sense of physicality and intensity. PES doesn't have the issue with weird ragdoll animations that FIFA sometimes has, but in terms of intensity and physicality, PES to me feels more like playing an int'l friendly match in comparison to FIFA. Again, to each's own. Personally I'm not sure which I prefer, as again its pros and cons for both, but again I find PES's approach somewhat limiting while the reliance on contextual shielding is really frustrating; on the other hand, I love dem fouls.
For me it's often difficult to say this game is better at this than the other, because they have such different approaches and priorities with their gameplay, and each has its pros and cons.
But what is clear to me is that Konami just doesn't have nearly the resources invested in PES to compete with FIFA long term, and so while I often tend to fall in love with PES upon release (like this year), after a while I always get this sense that I've seen it all while there's always cracks in the beautiful facade that begin to show after enough playtime. FIFA, while it's got no shortage of flaws of its own, keeps me going much longer because of the variety, while the non-gameplay features, like CM and the licenses, really help to sustain me beyond that first month of playing each year.
I could not have put it better myself