Yeah that happy ending. With starvation and disease rife. The odds against the quarians and turians fleets living long enough to reach a system with food they can eat.
Dear god you are right. Shepard and the crew meeting back up solves all of that. How did I never see it before 
It's a ray of hope against what would otherwise be a very bleak prognosis. And as Mordin said in the second game, it's hard to picture the entire galaxy... too impersonal. We have a character we(supposedly) emotionally invested in(Shepard) with the person that(probably) means the most the them(their LI) and we see they are happy, at least for the moment. That's what matters right now.
Sure, there will be strife, misery and who knows what else. But it leaves you with a hope that yes, things are good right now and can change for better. We've been through so much already and we don't know what will happen.
"The clock is running. Make the most of today. Time waits for no man. Yesterday is history. Tomorrow is a mystery. Today is a gift. That's why it is called the present."
A romantic notion? Certainly. Perhaps even a tad of a foolish one. But it works for me.