theres so many things the need to sort out. many of which people have already mentioned but i'll list some of them again....
1) sort the fatigue out. its just a joke at the moment
2) more injuries during master league etc lets be honest all clubs go through patches where they get 5,6,7 or 8 players injured at a time.(and this is TOTALLY different from fatigue)
3) more licenses would be great but i'm not sure if thats really possible for leagues like the premiership because of EA
4) bring back the international challenge from pes6 on the ps2!!! that was quality, i still go back to play it now
5) edit mode should be more accesible, more features etc
6) referee's strictness needs a bit of work, on the old games you used 2 be able to pick the ref and they all had varying degress of strictness (in theory anyway)
7) maybe linesmen getting decisions wrong? it'd be frustrating at times but so realistic.
8) penalties need sorting out and have done for years. they look rubbish, the animations for the players shooting, the keepers dives. fifa has a far better penalty system where you can set the power and way the players strike the ball yourself as well as a chip down the middle.
9) squad updates would be nice, EA can do it, so why not konami?
10) online needs to be sorted big time!!!! the lag is so bad at the mo, they've messed up the whole lobby system.
11) stats for some teams are very poor. arsenal are very underated
12) more variation in the way teams play. if a club like derby come to old trafford on anfield the chances are they'll set theyre stall out to defend, get men behind the ball and frustrate. yet on the highest difficulty even poor sides can start playing the ball around like brazil 1970.
13) bring back the trophy room!!! it was pointless but i liked it.
14) more stadiums
15) keep the dive! added realism, and it doesnt spoil the "beautiful game" because most of the time you get booked for it so it serves you right if your cheating scum!