Here's what I would like to see, I hope you agree....
Referees
Although the CPU allows every ref decision to be right (if you ignore tackle vs. foul) I think there should be more scope for ref errors and controversy. It would have to be done right though so obvious calls are still made correctly but with close calls the ref could make the occasional blunder. The same would go for linesman; the closer an offside decision is, the more likely he is to get it wrong. You could even factor in how far away the ref/lineman is from the incident, with more distance increasing error probability.
Of course, this would be an in-game option so you can still have "perfect" refereeing if you want.
I think it goes without saying that the decision making for fouls needs looking at, too often a foul is called when you clearly got the ball. The computer is making the sound of contact so why is it so hard to relay this info to the CPU ref?
Fans, Stadium and Coaches
It is obviously impossible (at the moment) to model 50,000 3D fans accurately but surely we can have a better looking crowd? In the screenshots for PES2008, the crowd are all the same and Konami seem to think that everyone who goes to a football game wears their team's shirt.
I'd love to see managers and coaches added to the game too, standing in the dug outs in the stadium. You could even link it to 'Teamvision' so when your team adjusts its tactics, your manager comes storming out to the sidelines shouting and gesticulating at the players to change tact.
Commentary
This is the one area I think every agrees on. It isn't the choice of commentators that bothers me (Trevor Brooking who hasn't been a pundit since the old MOTD and Peter Brackley who I can only vaguely remember commentating on Football Italia), no it is the quality of commentary that needs addressing first. I don't know a lot about computing sounds to fit events but some of their analysis is so far off it's embarrassing. OK so I'm not expecting Andy Gray to come on and give a unique summary of my game, but at least fool my brain into thinking I'm listing to a real person a little.
Modding Support
I know the PES series is primarily based at the console market but could we please have better modding abilities given to the PC community? For example, why can't you add more teams to the game? I don't mean replace, I mean add! I don't see why you can't add as many leagues and teams as your hard drive supports. Kitserver allows you to add more kits, stadiums, faces etc to current PES titles but if the actual game coding could be done to allow expansion and have user made kits integrated into the actual game, it would be better.
Stats
Why can’t Konami gets their stats for all players from Opta or someone? Instead they just make the big club players better than they are and everyone else a pile of dog poo. I would also like to see more attributes attributed to players so that you make players more individual. For example, as well as having Speed and Acceleration, why not have "speed when in possession" so you can make people like Kaka realistic as he runs faster with the ball than without!
This maybe the ultimate in wishful thinking, but I'd love to see a monthly patch released by Konami with all the latest Opta stats so you're game is always up to date. Currently, some of the players like Kaka are underrated and Adriano way over rated and you have to wait for the next game to come out before you get realistic stats again.....
Mater League
This needs to be much more expansive and realistic. Adopt a "Football Manager" style transfer system so a player can turn you down as well as the club. Make it so you have to agree a transfer first and then wages and have players hand in transfer requests etc. Oh and can we have our local currency please, I hate doing transfers in PES Points, it means nothing.
And why can't we have 20 teams in the Master League? 16 is stupid as MS is supposed to mimic Fifa's "career mode".
..and finally defence
I know everyone wants better attacking gameplay (close control, tricks, etc) but I would like better defence too! I think it is too easy to skip past people in Pro Evo I believe because there isn’t a realistic defence system. For example you can’t run backwards (as far as I know) and sometimes defenders just don’t perform instinctive actions when attacking players are near them.