Personally, I find that at least the red ending isn't all that bad, and it's greatest flaws could be sorted simply by cutting out content.
Everything up until the chat with the god-child, is fine. The chat itself? Horrible, but fine if in a slightly different format, meaning cut the child. Not sure what would be better, but kind of leaning towards a final chat with Harbinger to fill in that exposition.
And for the choices themselves, ditch synthesis, it's confusing and doesn't make any sense. It should simply be the choice of doing what you came to do and destroying the synthetics (paragon), or following the Illusive Man's dream and seizing power through control. I also think it wouldn't have hurt to change up the wording of the destruction option. Mainly, "destroying all synthetics" doesn't make a ton of sense, does it destroy all electronics? It's kind of important how that plays out.
Beyond that, the mass relay network being destroyed sits well with me if it weren't for the fact that exploding relays are supposed to wipe out a solar system, which would be fine with a minor dialog reference assuring that that would not happen and why.
And then there's also the matter of the remnants of the galactic fleet now more or less stranded on Earth, but whatever. I figure much of the fleet had been wiped out anyways by that stage, and it's an acceptable consequence for saving the galaxy. Besides, if the destroy option fries all electronics, they're dead anyways.
And finally, no matter how the rest plays out, get rid of the final scene with the Normandy. It's hard to make any sense out of how it would have happened and it just feels out of place. Replace it with a series of quick cuts to the characters still around, mostly on Earth, looking up at the exploding remains of the Citadel with a silent farewell to their Commander.
Anyhow, point was that I don't really mind the core concepts of the endings, they just get spoiled by some poor presentation choices.
