Yes. There are a few inaccuracies here and there in FIFA, but I would say that FIFA isn't that bad compared to PES. In fact, it's far better. I personally work with EA for the K League ratings (and I know one of the J League editors personally as well...) and we try to go through every player and make sure they're accurate and so what. The rating process is pretty systematic, but it can get a bit subjective from time to time (not all stats can be objectively rated) I agree that the J League and K League might be a bit underrated and the teams can be a bit higher, but overall, the J League is rated pretty fairly across the board. There are a few glaring mistakes here and there (of course, I hate them, and would love to have all of them fixed!) such as Hashimoto for Vissel (for pete's sake he's a 50 rated) and Leandro for Kashima (too high IMO). However, quite a few of these mistakes we can't really help with due to existing guidelines, EA headquarters (very bureaucratic) and such (I won't go into that because I've signed an NDA). It's really hard to fix the weak foot or positions in some instances, and others it's even more difficult. You can probably glean more on SoFIFA from the Belgian players, as the editors from time to time post justifications for the ratings.
PES ratings are often atrocious for non top league players (bar Japan) even on terms of distribution (let's not mention the over/underrating here shall we? Ex. Veron). However, patches ameliorate this problem, unlike FIFA that isn't so supportive on things such as option files. Also, Master League is a clear win vs Career mode (this is not an opinion of EA, but rather a view of mine only as first and foremost a football fan and a lover of video games). Faces might also be something PES is better at. In my honest opinion, FIFA is a video game about football. PES is a football video game (just my opinion!). This depends on how you take it.
I do have both copies of the game PES/WE and FIFA and I do enjoy both of them much, but for the ratings of players, FIFA is a clear win