Just spent the past two months playing and beating the three games and here's my shot at an ending.
I liked the concept of "Destroy or Control" but you shouldn't have been able to make that choice right then. Instead, what happened at the end should have been just a RESULT of your actions throughout the ME series. Basically another ME2 like ending.
For instance, if you didn't destroy the collector base and your Shepard survived ME2 the illusive man should have beaten you to the punch and already begun controlling the reapers. Imagine everyone's fighting and all of a sudden it stops with the reapers somehow announcing to you that its now the illusive man in control and everyone who isnt human basically gotta get down or lay down. From there, you can launch a final assault on him and the remaining cerberus troops and depending on your military strength you and your squad die trying or are indoctrinated or you get through. If you get to him with your whole squad intact, you can convince him to destroy the reapers and himself or you kill him yourself and destroy the reapers with the crucible based on your paragon/renegade ratings.
If you DID destroy the collector base and your Shepard survived ME2, then the illusive man experiences difficulty controlling the reapers. If your military rating is high enough then they attack each other, if not then they attack each other as well as everyone else and some of your squad will die. Once in the Citadel, you are confronted by the VI of the person you let die on Virmire. They tell you how to destroy the reapers but they say the Citadel will be destroyed in the process and one person must stay back and be destroyed with it. Someone on your squad will volunteer and if you brought the one that you spared on Virmire then it will be that person. Otherwise it will be whoever is closest to Shepard out of the two that you brought,if your people managed to survive that is. With a high enough paragon rating Shepard can stop that person and do it himself. If your whole squad is there then Shepard will manage to survive like in the extended cut.
If your Shepard died in ME2 then he/she dies here regardless of what you do and another squad member carries on your mission, whether it's the showdown with the illusive man or the VI.

with that Synthesis shyt.
there's some holes here, but this is the general template that I would have followed.