Simple. You do not try and top the Reapers. Not every story needs to be some huge and epic tale with the entire galaxy at risk. I personally hope for a story taking place shortly after the Reaper invasion and dealing with the current state of the galaxy and its efforts to rebuilt. Maybe told from the point of view of someone non-military. We have already seen the galaxy from the point of view of a Soldier/Spectre, now lets see it from the point of view of the everyman. Maybe the crew of small cargo ship dealing with their own issues. Or maybe Mercs, or just some schmuck who sets out on an adventure. The Mass Effect Universe is so full and rich with possible story ideas that anything could be possible.