Personally, I just feel changes should be made so that every mission takes at least five minutes to speed run.
Secondly, they should try to incorporate some sort of randomized branching mission objectives, so that missions might start the same, but have different outcomes for completion. This would help offset speed running, and also break the monotony that has occurred for people that have played every mission so many times, they have every objective memorized.
They could even merge the missions they already have to accomplish this task, as most of the time we will see the same mission multiple times and some missions very rarely, anyway.