i think since most of the archetypal missions have been made its important to keep a strong storyline and keep the missions well scripted and very replayable. its not necessarily that attacking a base is unoriginal but sometimes authors go about it in a really obvious way. the trick is to add gimmicks and surprises to spice things up. its like eggs - they are always good but its important to not eat boiled everyday, else it gets boring. another important thing is narrative, imho. identification with your character and his personality is usually a good way to immerse a player and make new ideas have even more impact. if you try to hard to come up with new plots, as you have pointed out, things just get way out of hand.