The online experience would be greatly improved by the following;
Stamina/fatigue being properly implemented - Got someone running round like a maniac chasing you down non-stop for 90 minutes? Pass the ball around, let the ball do the work while they exhaust and injure themselves chasing it, then pick them off with ease later on in the match.
It would also stop people abusing the "Speed Merchants" and sprinting down the wings all game, as they would become quite ineffective fairly quickly as well as increasing the effectiveness of players such as Ji Sung Park and Michael Essien who are renowned for their stamina.
Make defending more difficult - I like FIFA's idea this year of implementing a system whereby you need to press a button to tackle rather than just hold one down and home in on the ball carrier like a missile. Means you'd actually need to time your tackles.
Also reduce the effectiveness of the fucking slide tackle!!!

It does my nut in how difficult this is to counter in PES 2011.
Sort out referees - Kind of following on from the previous point here, if the refs called fouls and played advantage correctly, a more conservative and tactical style of defending would be rewarded.
It would also increase the number of free kicks and penalties to a more realistic level - I havn't had a penalty online for weeks, and free kicks in dangerous positions are few and far between.
Remove the exploits - Add a lot more error to triple-tap low crosses (crossing in general really), give "Speed Merchants" less agility/perfect touches (only Messi can truly dribble like the Speed Merchant card allows).
Make the "kick off chip" ineffective, and improve defender's awareness and ability to intercept constant quick passing as well as improved ability to track the runs triggered by the L1 + X pass.
Encourage variety - There must be about 7000 players in the game, yet only about 100 of them are seen in the online arena.
Maybe the amount of ranking points awarded could decrease after each consecutive game using the same team, and a massive amount of points lost for losing to a weaker team than yours?
Also a system so that in MLO you can only have the elite players by being successful in D1 would help, rather than just how it is now where you can get anyone no matter who you are, as long as you've played enough games.
Sheffield FC are the oldest football club in the world, and have probably played more matches than any other team, but you wouldn't see Messi and Ronaldo signing for them...
The effectiveness of certain types of players (especially target men) and tactics (especially deep defensive lines) should be improved to add further variety to the matches themselves.
Set "Top Player" as the default level for all online modes - As kobayashi has mentioned many times, this makes a huge difference to the intelligence of teammates.
The obvious gameplay/bug fixes - Ball physics, player switching, AI, reduced lag etc.