That isn't RTS.
RTS is real time strategy, well, a SC2 style subgame.
And while "mission A" or "mission B" is cool, I'm assuming they are cheapskates. So what actually happens is "mission A first, or mission B first" -- you can still choose to skip missions, but (if you are a completionist) what you pick is the order and priority.
And these choices end up having costs. If you go for the Turian commander before the Krogan genophage, when you finally get to the genophage, something bad has happened.
Have you played those "multiple players against the game" boardgames? Like that -- the universe is going down hill, and you are constantly trying to push back, but it just gets worse and worse. Everything you do is seemingly counterbalanced with something bad happening elsewhere. Worlds fall to ash, fleets get wiped out, information is stolen by Cerebus before you can get there.
Because we are lazy developers, much of this can be in the form of extra bad guys on the missions, and different information in the between-mission reveals. The value of the information you extract is lessened if you didn't prioritize it in post-mission analysis, for example, because Cerebus destroyed more of it before you got there. Or you manage to get there first, and erase some information to Cerebus doesn't learn something...
The nice thing about that kind of narrative is that instead of Shepard holding the idiot ball so often, she gets to competently doing what she sets out to do. What you prioritize works (usually) -- it just isn't enough
. You single-handedly destroy reapers (with the help of a fleet), and it isn't a pointless victory -- but while you where doing it, entire worlds have burned. Instead, the game jumps between scenes where you do that, and ones where you hold an idiot ball, all to keep you on a rail road to AB or C.