I can't re-call if I posted here or not but here we go...
1) MASSIVE WISH, the ability to set the leagues starting dates a year forward, not only would it make the game accurate it would also have the very nice subtle effect of cancelling all loans, injuries and the dread "Happy to have joined the club" statuses that shouldn't be there, making the game far easier for me and other editors to edit as we would just need to attack transfer, finances and promotions/relegations. You can not even begin to comprehend how much work you would save just me alone! Failing that a search filter for players on loan and one where you can locate players who joined clubs between two dates i.e. "1.7.2009-31.12.2009" so I can at least do my editting a hell of a lot quicker!
2) Being able to change the type of ownerships at clubs, i.e. having a fans trust, set ups similar to Barca and Real and so on. I.e. the President has to be elected etc.
3) More editting ability for competitions, the ability to edit continental competitions as others have said.
Really for me its the first one in such a massive way I'd probably cry if it was implemented due to the hours it would save me!