It would enrich the game if a mission's reward changed with the path/s taken by the captain throught the episode. This seems to be the general consensus amongst the forums.
The furthur addition of a 'timeline' during episodes would make the missions feel "live" and real. Do you pursue the ship carrying the kidnapped ambassador, or beam down to the planets surface to deliver your life saving mission payload? Do you have time to do both if you are quick?
Similarly to the current Feature Episodes, say, a checklist of 10 total objectives, but your episode journey takes you through only 6 completed objectives, (maybe you missed a secret side objective!) you could recieve 6/10 ths Maximum mission experience plus the finishing experience or material reward. Perhaps each objective could be weighted seperately depending on the complexity / difficulty of the objective.
As the icing on the cake, could you recieve a hail from Starfleet Command at the conclusion of the mission, which reflects your performance and judgment regarding your mission score. AKA the TV shows, movies, and old-school StarTrek games!
These features would give content authors the option to incorporate depth and variety at an early stage of the Foundry's development.