But that's not the logical outcome of the trilogy.
Yes, it is. Billions of years of successful harvests and conquered advanced civilizations says so.
the breath scene isn't really an ending though. It's a little extra tagged onto a (lower EMS) ending that already exists. It's an easter egg.
Still the most difficult thing to obtain in the game.
And EDI's speech says nothing about these potential pitfalls (which you rightly identified) There is no hint of it anywhere. Everything is shiny, everyone is happy. Mary Poppins is running the show, because everything is practically perfect in every way. The only unsettling thing about it is how blatantly over the top upbeat everything is. Reaper tech is AWESOME now!
Eh, do a little extrapolation from the things you see in the Synthesis ending, and exercise some rational thinking. There's more than the upbeat, even if BioWare opted against showcasing the grim in the endings (something the fans absolutely didn't ask for). Dragon Age didn't showcase the potential repercussions to the OGB, either.
Yes, core ideas are core ideas. And that's why these endings suck.
Then the trilogy was doomed from the beginning, because both original and new lead writers were headed to a similar point. Not to absolute power-fantasy.