The very short version I eventually decided on was that the endings presented at face value were stupid, but the Indoctrination Theory take on it was less stupid.
The endings presented at face value are broken. Straight up. Plot holes abound like characters aren't where they're suppose to be and your team, along with Joker, wouldn't suddenly abandon you. I chose the unification ending as the lesser evil, which ended up being space magic which makes absolutely no sense in the context of this game when it's been trying so hard to be the sort of sci-fi that's something like believable. But more than that, the choices were non-choices that thematically don't fit the game. The synthetics vs organics 'central' theme they're based on are contrary to much of the trilogy and is more or less sprung on you at some point in ME3. None of these ending are much like a victory if you think about them either. Control was all sorts of sketchy, and destruction was...trying to be some sort of lesser evil that still doomed trillions? And I'll even buy that the relay net going down doesn't vaporize everyone in the galaxy, but they all basically do the same thing - Reapers are removed by imposing your will upon most to all of the galaxy to disastrous effect. You basically do what the Reapers set out to do in a flash rather than over a hundred or so years of intense war. It's the sort of copout you get with bad writing trying to grope for some sort of 'higher plane' of choice and effect when it hits a wall with where it's at, and then fails, hard.
None of it particularly makes sense or flows from the rest of the games, and none of it really achieves the goals you set out to do, and none of it particularly honors, nevermind plays into what's gone before. You get a 'new beginning' on the Reaper's terms, which is what would have happened anyway if Shepard had done nothing (barring the Reaper's destroying/uplifting humanity if left completely to their own devices).
Then looking into the Indoctrination theory, I had to admit it makes sense in that the whole sequence of Shepard getting to the ascension beam and everything after is very dreamlike. Slow motion husks and only getting shot once by the Maurader who then mostly sits there until you kill it. Never having to reload. The Illusive Man just showing up at a critical juncture. Joker fleeing with the Normandy to crash land on an alien world with the very people you took on this final mission with you. The Illusive Man's compulsion effect is very similar in style to Shepard's nightmares at that, nightmares that are trying to say something but don't really serve any thematic purpose other than to lend weight to the Indoctrination theory with the visual effects, chasing the child/burning, and all the shadow people surrounding you, talking about/at you, haunting your dream like Reapers just might do with Indoctrinated people. Even more telling is that Shepard's corpse starts breathing again if your galactic readiness rating is high enough...in the rubble on earth, which would be a special sort of stupid if Shepard had actually been on the Citadel as it blew up and then crashed into the planet. This really suggests that your war efforts saved the day in the end and none of this catalyst BS was anything more than death dream mind games.
It cheats, but it's less stupid, and fits more with Bioware as I perceive them.
And then I thought back to the Reaper's doom beam intercepting Shepard at the beginning of the end, so s/he should just be dead and all of this is total bullshit anyways.
What makes me really mad at this setup, and Bioware and EA in general, is that I was told this was the ending of the trilogy, but it probably isn't. It seems they're just playing with our emotions to get 80% of us to buy more DLC and get the 'true' ending at some point down the road.
I am a special sort of bitter about this.
As for my personal ending, I'd go with everything up to Anderson dying, then have Shepard more slowly bleed out as you watch the armada you've brought together and your friends and comrades grind the Reapers down to dust. They cross the finish line without you, because of you and all the other sacrifices, but they do it. And Shepard's reward is to watch this as s/he dies. (Or maybe Shepard gets saved in just in the nick of time if you went completionist on the game.)
Sorry, Susan, but I think most people who aren't happy with the ending are like me and weren't expecting a 'cake!' ending, are definitely not demanding one, and only sorta envision/want one for that gamer completionist/catharsis/I damned earned a happy ending at this point sort of way. That said, a creator has a right to define their creation any way they see fit, but that creation can still be utterly broken and wrong.