If there's one aspect of games that rarely has much replay value, it's missions/quests/jobs. At best, some games allow you to choose between dialog options or one of a few scenarios, but those dialog lines and scenarios are strictly scripted and play out basically the same way every time.
Let loose your iron grip, game writers!
I've said it before and I'll say it again: adventure is about the unexpected. Adventures often begin with well-defined goals, but they absolutely always involve unforeseen events and events of chance.
The best path for stories in games is reflection, not determination. Rather than determine exactly what the player will experience, provide a solid setting with many dynamics (including dynamic NPC choices). Then record and present special moments (not entirely scripted moments) for reflection at the end of the game or levels, areas, etc.
Setting and reflection, how events are viewed and fitted together, are the key elements of story in games. Don't feed me the story. Let me live it!