Actually, the extended cut clearly shows the rebuilding of the relays even in the destroy ending (ie: the only ending you should ever pick). And the Catalyst says that "though some technology you depend on will be damaged, you will be able to repair it easily". Not that you should trust anything the Catalyst says, since it's a traitorous, evil AI built on universal annihilation of all life. BioWare retconned the endings because of the complaints. The galaxy is not fragmented without the relays in any of the endings.

Although how they could possibly set it afterward is going to be interesting. I mean, pathetic as the choices were, there are some far reaching implications. How would you play out Control, Synthesis, and Destruction carrying over into a new game? That's a far bigger change than some of the others, which BioWare only paid lip service to.

Then there's the romance choices. If Shepard paired up with Liara or one of the humans, there's the potential for children going forward (especially if Shepard romanced Liara or if you pick the Destroy ending). How would they play out Shepard's legacy/family? (SPOILER)Although I'd love to play as Shepard and Liara's Asari child if we're going forward, but then, my Shepard romanced Liara, and not every one did.

Do they declare one particular route to be "canon", alienating everyone who played a different one? Do they have the differences turn out to be minimal despite their galactic impact?

I'm really quite, quite interested into where this is going to go. Mostly because I think it's going to be horrible.