I believe as well, and is no question of faith. Battlestar galactica did something like this and was... weird.
This endings are the SAME provided at Isaac Asimov's Foundation books. In the book there was:
"Help person 1"
"Help person 2"
"Sinthesys" (Or whatever is written on english)
So, if we also compare with the "Deus Ex" first game, is the same ending. SAME.
No question of understanding or not, you can understand anything if you think enough time. Other fact is that in the 99% times you will be wrong about the things you can't understand.
The ending was awfull in all cases, senseless, with no argument but "the reapers win no matter what you do", without roleplay, plenty of mistakes and nonsenses... and more.
If you see carefully, even a LOT of elements are taken from ME2 development, what evidences LACK OF TIME in the artistic and development phase.
Another thing: if you understand the endings, tell me something.
How the hell is possible for the Harbinger, a killing machine experienced with millions of years of wiping out entire civilizations, miss a killing blow against single the creature that is close enought to destroy them?
Is Harby blind? his sensors are damaged? is he silly? "That was a joke"?
If you think how the ending is developed, it lacks of many things. A Normandy rush to cover sheppard is logical, as well as suicidal, but nope. The Harby only "walks away", to let sheppard kill, control, or "have a ring to rule them all".
The endings are no matter of faith (God has nothing in common with the idiotic star child), is matter of "obvious senseless".
To end my complain, thing that God does the things with a sense. And without plot holes.