Most of mine are to do with the match engine, which I pay a lot of attention to...
1) The amount of free kicks and especially throw ins that go directly to an opposing player is insane. A lot of the time they are thrown right to an opposing player with none of your players anywhere near them, as if they are returning the ball after it had been put out.
2) Players attempting bizarre passes. A lot of the time I'd see a player (say a striker) collecting the ball down a flank, and then trying to play it down the line in front of him for the winger who is running behind him. Always going out or being easily collected. No player would attempt a pass like that.
3) Players attempt long shots too often on the default "mixed" setting.
4) Players attempt to shoot too often from free kicks from ridiculous distances/angles. Sometimes when there isn't even a wall.
5) Two players constantly passing between each other and losing the ball happens quite often.
6) Players do not seem aware of their own abilities and weaknesses. A player seems to have no hesitation in attempting a long shot on his "very weak" foot if play opens up for him, even if there are people to pass too. In real life players are usually very wary of attempting long shots with their weaker foot.
7) A combination of some of my other points in that I feel the "Run With Ball" and "Try Long Shots" instructions strange. If a player is good at dribbling they should run with the ball, and if a player is good at long shots they should attempt them. They should know this themselves and it should be obvious.
Getting away from the match engine....
8) This might be a controversial suggestion, but I'd like to see some kind of "Potential" attribute for players. Right now it is really juts impossible to sense a potential of a player unless you scout them, and hope they are accurate. It's not like real life where you see the player in training every day and can get some kind of "feeling" if the player will be special. I don't want an exact numerical description as they are in the database. But a one word description as in "High" or "Moderate" would be welcomed by me.
9) Player interaction. Right now, to me, it just seems... totally random. I can praise a player for his good performances and he's delighted, I can do it again 2 weeks later and all of a sudden he "Feels under pressure to perform". What changed? It just feels like a lottery now.
10) Crazy chairman.I don't know how much this happens in real life, but your chairman splashing out Â£18m on a Central defender when you already have 5 that are better is very annoying. If they are going to take it into their own hands and sign someone they could at least ask for suggestions.