For almost three years I felt like PES 6 was the alpha, and there was no other game better than it. This was of course because it's the most well-known game from the PS2 era and everyone say it's the best PES ever, and that was what attracted me to play it 3 years ago, and I didn't stop playing it until my last proper Master League.
That was before I tried PES 3 and PES 4 in a more complex way (I had played them before but like 5 exhibition matches and then bye bye, I hadn't given them enough chance before).
All my best MLs were in PES 6 and the memories will always be there, I can't deny it, but nowadays I changed my mind and no longer think PES 6 is the best PES.
And about PES 5, well after a year playing it and trying it and giving it lots of chances just to delete it again and go back to PES 6, I can oficially say it's my least favorite game from the PS2 era (at least from the games I played, I never gave PES 1 and PES 2 a chance because well I'm too lazy to download an emulator lmao).
I felt PES 3 & 4 were more fun, and both have lots of things that make them better than PES 5 & 6. But the most important one:
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Okay now seriously: after playing lots of PES 3 and PES 4 the past 12 days I came with my conclusion: PES 3 is really an interesting game, I like the graphics, it's notable that they're not the same as their 3 sucessors. The Master League is more organized and at the same time not so organized: we've got the leagues already designated in a very unique way, but at the same time all the teams from the 2nd div are just random, and they're always the same, you can't change anything. That is a bummer. Like, on one hand I like how the game just makes everything for you like saying "okay man just have these leagues and play with these players, and just play them like this idc" and I like that they're not like in the other ones where they have like three leagues with all teams from the the same country, and then they just leave a league out. That doesn't happen in PES 3, every team is included, even PES United and WE United. I like that because I can't tell how many times I got pissed with PES 5 or PES 6 for leaving the La Liga or Serie A out, and how because of that I always felt the need to unlock the composition. But of course PES 3 has some things I don't really like. The first one being that there's no full leagues in it. And because of that you cannot play a full Premier League, or Serie A in League mode. Then, the ML kinda confuses me. It seems different to the other MLs, like the wages are paid after every game (or that's what I saw) and I don't really feel 100% comfortable with that. And finally the least important thing I don't like: Real Madrid and Barcelona not being licensed. I have been so used to have both those teams licensed, that having them as Chamartin and Cataluna makes me feel kinda weird.
On the other hand PES 4 has full leagues, thing that I love, and like other person said previously, it gives you more freedom. The gameplay is really fun, compared to PES 5 and 6 I think it's better. It's less messy than PES 5 (I hate the PES 5 gameplay, it makes me so uncomfortable), and less robotic than PES 6. The background music in my opinion is the best one, plus I had gotten kinda fed up with the funky edit mode music in PES 5 and 6. On Master League you are not obligated to play with the default players like in PES 3, and you can actually create a team from scratch instead of grabbing PES United or WE United and editing them. Plus one really cool thing is that it doesn't matter if you create a club, pick an unlicensed club or pick a licensed club, you will always be able to edit everything on preseason. You can grab Atalanta for example, and after a season you could invent a history about a takeover at the club, and then create a Red Bull-like logo, and voilá you have now RB Atalanta after the takeover. One of the things I really don't like about this game, is how when you have a free kick or a corner and decide to pause the game, when you resume it the player just kicks it without you asking, and it's annoying because he doesn't even kick it properly, he just gives a shitty pass forward and ruins your chance that way.
So after what I said, this is my opinion nowadays:
PES 4 > PES 3 > PES 6 > PES 5
to pass further but the shooting wasn't as balanced or satisfying.