The problem with any rewriting is that the two writers who cared, Drew K and Chris L'Etoile, aren't there any more. Everyone knows Drew since he was the head writer and I don't know if he could have made it a great ending, I think he would have made it coherent at least. For me, the best thing would have been leaving the Reapers as Space C'thulu and never actually answer why they do what they do. Hell, I'd never have another Reaper show up at all, just have some contingency that wakes up sleeping servants and lean heavily on Indoctrination having everyone turn on each other. You don't need the physical Reapers. Could also have a great scene with Liara lamenting they never found out why the Reapers do what they do and just have everyone else call her a nerd.
Chris L'Etoile was also a huge loss. He wrote Ashley in ME1, Thane and Legion in ME2 and left after he couldn't get along with Mac Walters after he became head writer. If you want to know why those characters felt flat and not right in ME3, it's because he was gone. He was also the autistic nerd who wrote all those great planetary blurbs when you were exploring.
But yeah, remember that whole Dead Reaper mission in ME2? That, but expanded for two games. Robot Space Gods can't be gods if they explain to the ants why they're smashing them.