Gameplay wise Pes is superior in every way to Fifa, it feels more slick and responsive in comparison to Fifa which to me the whole gameplay feels slow, heavy, one dimensional and completely scripted (slow defenders always able to catch up to speed attackers). Fifa is and has been for some time now completely focused on Ultimate Team with the single player career mode hardly changed or brought anything new to. Pes Master League is rather iffy, however I quite enjoyed Pes 2013 in the fact you could earn points to unlock better player boots, skills and equipment like stopwatches to allow player stats to increase faster and better, the transfers were terrible though where each player had a % chance of buying and that never seemed to change, you could win the league and cups 5 seasons in a row and still the likes of Messi's chance of buying him would be stuck at 2%
On the other hand though Fifa comes with all/majority of the licensed teams, but lacks Europa and Champions League unlike Pes, and transfers ruin it by been too easy to sign superstars and unrealistic targets. Pes 2014 was a complete shambles on PC, Pes 2015 was a big improvement however the problem with PC users been shafted was a big let down (eg no HD graphics unlike the console versions).
I like the flow and gamplay of Pes, I like that it has the proper Europa and Champions League, I don't like the fake names and badges (without patches), The graphics look really dated, I don't like that recent versions of Pes seem to be against PC users, the Fox engine they kept screaming on about seems like false promises to PC users.
I hate the feel and gameplay of the Fifa, but I like the presentation of the menus and tactic screens etc, I hate the commentary of Alan Smith and Martin Tyler drumming on about the same rubbish, I like the official team names and logos, I don't like the unofficial cups.
Long story short, Fifa, Football Manager and Pes should join forces and make the ultimate footballing game
But as that won't happen, Pes remains the winner againt Fifa in my opinion, but as others have already said it's killing itself off with each PC release.