The thing that i have ALWAYS wanted to see implemented is the 'evolution' in competition structures over time in-game. For example, the Premiership might change from a 20 team comp to an 18 team one at some point in the game, or even to 16. Or the number of relegation spots might change from 3 down to 4 down in response to championship teams performing better over a period of time; the number of points for a win/draw might change too. Similarly the World Cup or Champions' League may expand or change in format, in response to teams from certain regions performing better (ie more spots for African/Asian national sides).
All these would add variety to long term games. It can get rather dull having EXACTLY the same format for competitions in 2050 as you do in 2007. And for those who really want the 'realism' (although im not quite sure how they're meant to know what competitions are going to look like 20 years from now) you can have the option to turn the feature off.
However, i'd imagine that this idea would be difficult to code, and the potential for bugs would be pretty high...but it would certainly add some interest and 'non-linearity' in the long-term FM game.