If handballs are reintroduced, they better be massively improved from PES3 ones. Every time I had the ball in a good position to shoot around the penalty, the defender got one foot in, and the ref blew for a freekick.
More national teams are needed, and ones already found in previous games shouldn't be removed. Bring back Jamaica! If more aren't added, the ability to edit national teams.
Volleying system to be more differentiated from headers. Too many times have a gone in to volley a rebound, and the player leans forward to header softly instead.
Quick throw-ins and corners to be added (like quick free-kicks) so the other team has less chance to get back.
As many created players to register to club teams as to national ones.
More skin tones in edit mode. Short-sleeved shirt, with long-sleeved top underneath (like what Matthew Taylor wore for Portsmouth earlier this season).
More highlights to be shown during half-time and full-time. More angles to view these from and slowdown of important parts. Also, in league and cup modes, names of scorers in other matches occuring at the same time, and a "league table or cup draw if things stay the way they are".
Power bar for tackles i.e. to go in hard, risking injury on self or other player and booking or sending off.
Ability to use logos already licensed in game for other teams (like Nike tick licensed to Arsenal, for instance). Crests on shorts. League crest editor.
Finally, although this is probably going too far and will likely never happen until the earliest a few years down the line on the PS3, use of eye-toy and microphone to make faces (briefly glanced upon in This Is Football 2005 I think) and to enter commentary name for players, team, etc, instead of when teams like Tottenham come out, they are called "North London White". Use of microphone to make own commentary phrases (where list of commentary has sound test, then can be edited).