There are a few things I think could be done to make the game better and more reasonably 90 minutes.
1) Timing done off the field. Is done this way in U.S. colleges and works wonderfully. Ref simply blows his whistle and crosses his arms in the air and official clock is stopped. Everyone knows time is stopped and teams stop time wasting!. If team continually time wastes, it becomes immediately apparent by the ref continually having to stop time and yellow card ensues. Again, it quickly stops!
2) Goal line technology. Long past due, especially given what has been at stake for recent calls (World Cup vs Germany, FA Cup Final, relegation, etc...)
3) A "red flag" review, possibly two per half, from coaches on plays they think are game-changing. For instance, the Zaba "penalty," the Shelvey red card that Evans did not get, etc... Hawk Eye does this superbly with tennis games and video review is used consistently in the NFL to good effect.
I don't believe any of these would substantially affect the running of the game, only the outcomes, by making them more certain and the decisions more transparent.