If we pretend like the indoctrination theory is false, and we're really supposed to take the ending at face value, this entire game is a lost cause. The krogans will never repopulate. The quarians will never rebuild their home world. The geth will never know what it means to be alive and independent. The salarians will never see how people can change for the better.
Instead, the quarians and turians will endure a quick, torturous extinction as they slowly starve to death, trapped in a system with no support for them. Everyone else will squabble over the scraps of Earth that haven't been completely obliterated, until the krogans drive them all to extinction and then die off without any women present. And this is all assuming that the relays didn't cause supernova-scaled extinction events simply by being destroyed, like we saw in Arrival.
And perhaps the worst part is that we don't even know. We don't know what happened to our squadmates. We didn't get any sort of catharsis, conclusion.
And then we're supposed to believe that the fate of the galaxy comes down to some completely unexplained starchild asking Shepard what his favorite color is? That the army we built was all for nothing? That the squad whose loyalty we fought so hard for was all for nothing? That in the end, none of it mattered at all?
The indoctrination theory doesn't just save this franchise: it elevates it to one of the most powerful and compelling storytelling experiences I've ever had in my life. The fact that you managed to do more than indoctrinate Shepard - you managed to indoctrinate the players themselves - is astonishing. If that really was the end game, here, then you have won my gaming soul. But if that's true, then I'm still waiting for the rest of this story, the final chapter of Shepard's heroic journey. I paid to finish the fight, and if the indoctrination theory is true, it's not over yet.
And if it's not, then I just don't even care. I have been betrayed, and it's time for me to let go of the denial, the anger, the bargaining, and start working through the depression and emptiness until I can just move on. You can't keep teasing us like this. This must have seemed like a great plan at the time, but it has cost too much. These people believed in you. I believed in you.
I would prefer to see the endings that were originally intended, leaked or otherwise i refuse to view leaked content and im sure many fans prefer to see things for themselves also, rather than being told. If that is no longer an option what i would like to see is a more rounded result based upon the players choices.
One of the more obvious would be an ending where everyone dies, and the war is lost to the reapers, by this i mean the loss is not implied but shown, for example showing the fleet in orbit of earth be defeated without the need support that the player failed to recruit, with the loss of the fleet the reapers would be free to wipe out the ground forces ultimately subduing the allied forces, possibly showing some of the iconic locations from the ME universe such as ilium or omega destroyed, while not everyone's favored ending it would give the players the closure they have asked for.