It wouldn't have been that bad, actually. It's largely a flip-flop, a race/character made it or they didn't. In which case you have a state for either. Quarians didn't make it? No Quarian fleet on your map. Character didn't make it? Can't visit them wherever they'd appropriately be located. Not knowing the outcome of all…
I think there are two issues here... First and more importantly, Bioware has not managed to execute their intentions as well as they should have. There's no need to explain this, I think ;) Second, and I don't mean to offend with this, they also overestimated their players a bit, most people weren't ready for this kind of…