An idea I would like to see implemented would be differences in Chairmen and clubs.
Like Real Madrid for example. We have a President, which goes up for renewal every 4 years. So do Barcelona and Athletic Bilbao. Now with these clubs, new presidents come in and do different things. Its the same at Chelsea compared to United. Alex Ferguson has free reign of Old Trafford and gets to pick and choose everything within the club, were the long list of prior Chelsea managers haven't.
What we could do is have someone like Abromovichs personality brought into the game. We he would buy a player, he would put pressure on you to play players and basically not give you much options other than outside of picking the tactics and selecting the squad. Not naturally he cannot force you to put the player in the squad but could send you a cheeky little memo saying he thinks Torres should play today and if you didn't play Torres then your rating with him would decrease, 10-fold if you had lost that game.
Players going over your head when they are not happy because they do not respect you as much as previous managers. As a manager coming into a side of say Real Madrid. You have Higuain and Benzema and your only planning on playing 1 striker but you dont want to sell either of them so your testing the waters and find Benzema is good to start with and Higuain gives and epic impact of the bench. Higuain could be unhappy about this and instead of come to you, he could go to the president to which the president could put pressure on you.
Now naturally not all chairmen and presidents are like this and some are quite the opposite who are happy to sit back and allow you to do your business and naturally there is alot more of them than the meddling ones.
Also with the meddling ones, once you start winning trophies and getting a reputation for yourself, your chairman will start to listen to you more and take your ideas on board, upgrade youth, training, stadium, and your players will have an increased relationship with you accepting his place in the team.
Sorry if its been mentioned before but something I have been thinking about.