The idea, or at least my idea, is that the final battle is fought on two fronts. The fleet of the galactic alliance against the Reapers near the Citadel, and then Shepard and the Normandy crew enter through an ancient hidden relay that takes them to a weird never before seen place that's linked to the Reapers and in stopping them.
They could've easily had written that the Reapers don't just literally chill out for 50k years in some random empty area in dark space, but instead do have some sort of base of operations or meeting ground that's out there. Even though the movie sucked, think the Machine City in the Matrix. Doesn't have to be exactly like that, but just the idea. There would've been great potential for level design, storytelling, final boss, and a satisfying final mission worth of the entire trilogy. And yes, that "base" would've been colossally huge and terrifying.
Instead we got a few fire fights on the streets of London while we hear everyone on the radio going "Ahhh the humanity! We're dying by the bajillions, the Reapers are invincible!"