I actually think the ending to ME3 would've been awesome as a combination of what we actually got for the ending, and the Indoctrination Theory.
In other words if you played the games poorly you get access to just destroy, or if you played them very well, then you get access to all three endings. The endings would then play out exactly as they did in the Vanilla. Just different colors, very minor variations. But if you played through the trilogy to your absolute best ability and made the correct variation of choices, you get access to the true ending, which is Shepard breaking free of Harbinger's control, and then proceeds to use the Crucible "correctly". What do I mean by correctly? Well I don't know, I'm not a writer, but it would basically be the ending where you blow the Reapers to kingdom come, no strings attached.
The entire trilogy always kind've implied that Shepard would eventually become very vulnerable to Indoctrination, and then in ME3, there are definitely signs of him showing the effects of indoctrination, whether that was intended by the developers or not. Why the writers never pursued this, I'll never understand. The ending of ME3 should've messed with the player's mind. It should've been an effort made by both Shepard and the player, to win a battle of will against Harbinger or The Catalyst, break free from control, and win the day.
Or maybe that's too video gamey. But I really think Bioware blew it with this one.