Here is my thing:
The Reaper's Motive for extinction needs to be scrapped. It is the seed from which all the complaints about the game's ending stem. Their motive is to exterminate organic life from the galaxy because if they don't synthetic life will exterminate organic life from the galaxy.
WHAT?
First, that doesn't make sense; you have the Reapers doing exactly what they say they are trying to stop. Unless you operate under the assumption that the Reapers don't exterminate ALL organic life, whereas other synthetic life would...I guess theoretically destroy ALL organic life to a bacterial level? Which doesn't make a whole lot of sense either.
Second, why are we suddenly supposed to accept as fact that it is true that all synthetic life will eventually destroy organic life? The only synthetic lifeforms that have actively tried to destroy all organic life are...the Reapers themselves. The only other example we have is the Geth, and there is no concrete evidence from the Geth to support the Reaper contention. In fact, it's quite the opposite.
In my opinion, I think they should have never given us a motive for the Reapers. Why do they want to kill us all? Just because. Because after all, the enemy you don't understand, the enemy who's motives are so utterly alien that they are beyond your comprehension, now that is truly terrifying. Heck, I would also have been ok with just operating under the assumption that I had in ME2, that Reapers needed to use us to create new Reapers. That's fine too.
By removing their motive, it removes the need for the god-kid AI who explains all this crap, and the need for the 3 choice ending.
I think then there could have been a plethora of endings
1. You failed to bring peace to the races of the galaxy. The Reapers defeat you and life is exterminated from the galaxy.
2. You failed to bring peace to the races of the galaxy. The Reapers defeat you and life is exterminated from the galaxy. However, you left some message for future generations of the next cycle to give them a chance.
3. You use the Crucibles magic McGuffin powers to Destroy the Reapers, but at heavy costs. It is a phyrric victory, society still crumbles, but the Reapers will never threaten an organic race again.
4. You use the Crucible's magic McGuffin powers to Destroy the Reapers, and the galaxy survives, but because you failed to truly bring peace to the races, without the threat of Reapers over there heads, soon the races of the galaxy seek to exploit each other in their weakened state
5. You or the Illusive Man used the Crucible's magic McGuffin powers combined with the Illusive Man's study of Reaper tech you saved on the Collector Base to take control of the Reapers and conquer the galaxy for humanity.
6. You unite all the races in the galaxy in a true alliance, Destroy the Reapers, bringing true and lasting peace to the galaxy, but at a high cost of life.
7. You unite all the races in the galaxy in a true alliance, Destroy the Reapers, bringing true and lasting peace to the galaxy, and Shepard survives the events.