It's the licences that put Fifa ahead mostly. Plus they've really been successful since Ultimate Team came in. I know PES have their own version but UT is extremely popular and it's hard to compete with that. I haven't played it for years but I expect the overall gameplay of PES to be much better.
Pes3 might be the greatest football game ever, well after indoor football I enjoyed pes4, wasn't a fan of 5, liked 6 and then got a demo for pes2009/10? Whichever came after pes6 but didn't like it 1 bit and made the switch back to FIFA
ISS Pro Evolution 2 (early version of PES) on the PS1 was one of the best football games ever (if not the best). I don't know if anyone has played it but it was great at the time. All the critics raved about it and rightly so. This was like 11-12 years ago though, so props to anyone that did play it.