Well I've been putting this off for long enough. Guess I'll just toss out my personal feelings on the ending.
In general I have no problem with how you wanted things to end up. I can sorta see how you wanted to steer it. The issues I have are mostly with how you try to shoehorn it in there. I'm going to avoid the "plot holes" and "doesn't make sense" stuff, all that has been covered by other people far more eloquent than I am. I'll just deal with how I felt on playing through priority earth through the end. Yes it's a disorganized mess. Then again so am I.
#1 - Let's just get this over with early. The ghostly figure of the child that pops up as the "Catalyst". You introduced this last minute with no foreshadowing (unless we count a single entry in a planetary description in ME1). It's immersion breaking when something like that just jumps out and kicks you in the metaphorical daddy bags. Not going to tell you how to do things, but that one thing messed up a lot of what you had going. It just doesn't feel like it fits at all. Maybe I'm just an idiot and the dream sequences were supposed to make it palatable but honestly those felt more like internal guilt trip character building than plot driven foreshadowing.
#2 - War Assets. Yeah, you guys know what we want here. I'm guessing money/time is the reason we didn't get it. I'm gonna give you the benefit of the doubt here. (
Combat drop a Geth Prime onto a marauder in the EC pls.)
#3 - The first area of the mission was good for me. I actually thought "STEEEEEVVEEEEE" was pretty funny. The break in action at the forward base was ok, HOWEVER the turret event completely broke the pacing for me. Would have liked a bit more background chatter between the factions based on your accomplishments (Krogan/Turian with the genophage cured, Geth/Quarian reconciliation). The areas leading to the missile defense area were kinda bland. Honestly I felt like I was playing FEAR or something with the level layout. Missile defense event was fine, felt pretty badass ripping through so many banshees.

#4 - The rush to the beam. Ugh. For some reason this entire part bothers me. On some level it just doesn't fit. This is where the end begins to disjoint from the rest of the game and goes from "Well, it's mostly ok." to "WTF are they serious?". The actual run to the beam kind of built up the feeling of "Hell yeah everyone else is dying but I'm a badass!" when it first starts. Then you get hit by Harbinger. Total curveball, BUT perfectly understandable. At this point it's "Oh hey they must be going in a different direction with this!". (Which starts hopeful but ends up feeling like a total kick in the balls.)
#5 - Post Harbinger. Ok wounded, staggering to the beam, only able to use a pistol (which I wasn't even carrying

), and generally looking like it's gonna be a "heroic sacrifice" type of ending. No prob there, I read a lot of "Grim Dark" Scifi so I'm used to it (also used to seeing the hero fail anyways

haha Grim Dark). Citadel is a charnel pit, ok let's move on. Anderson is alive? Wait... what? This is where I feel confused. Hammer got pwned, you went in BEFORE Anderson, he ends up ahead of you and command thinks everyone who tried to go to the beam failed and is dead. Great, then how is he ahead of you, how come you didn't see him running after you, and why would the teleporter beam be randomly zapping people to different places? Ok moving on.
#6 - Anderson and TIM. My first thought was, "Wait. We get hit by the beam and
he's still got his damn hat on and it's in one piece?" I mean Shepard looks like he got run through a meat grinder then popped in a giant toaster, but Anderson's gear is fairly undamaged? And somehow Shepard made it in first.... in hobble mode. Then apparently TIM somehow learns to control people's bodies using reaper tech. That's fairly out of nowhere. Indoctrination doesn't mention hitting the body BEFORE the mind. I mean if reapers can do that why don't they just have everyone line up single file and march towards the banshees? Ok we get through that part. Anderson dies, Shepard is bleeding, and suddenly Admiral Hackett is on the line trying to tell you to do stuff, even though he thinks you're dead. Moving on.
#7 - Space Kid and the Magic Elevator. Ok so the reapers are controlled by this thing. Greeeeeaaaaattttt. Why are we doing what it's telling us to do? Why aren't we trying to figure out where it's main memory core is and destroying it? Why isn't Shepard trying to destroy this thing/convince it to destroy itself? This entire section feels like it isn't even the same game. It's almost like it was jammed in at the last minute to "give choices" but the choices were hollow. There's no expansion on what happens after the choices, there's no explanation given as to WHY the space kid is giving you these choices beyond "Oh hey, you made it up here. Congrats." I seriously got the image a little after I finished the game of some poor salarian janitor accidentally finding the elevator and having to decide what happens to the galaxy. The various methods of selecting an ending seemed.... forced. I mean it seemed like they were only there so it
wouldn't be "Green button, red button, blue button."
Honestly, if you wanted to end up with a "Galactic Wasteland" there was no need for Space Kid. If you wanted the relays destroyed/burned out, there was no need for that last section. You could have just ended it with Shepard and Anderson dying on the citadel and the Crucible activating and causing Control/Destroy/Synthesis purely based on EMS. That stuff just caused me a lot of annoyance as I had to sit there and sort through why I felt like I had just been kicked very hard...yes... in the balls. You guys hyped a lot on choice, you hyped a lot on it being the END OF SHEPARD'S STORY. And most of all you said that because it was THE END you could do a lot with it that you couldn't do if you were going to continue the story, i.e. "Wrap up all the loose ends."
It feels rushed. It feels like there wasn't a lot of choice at the end. It feels like you wanted to just "cause speculation" for it's own sake, and it feels like it wasn't worth $70 for singleplayer. Thank god MP is actually fairly fun or I wouldn't be getting my money's worth. The EC will be the deciding factor on my future Bioware purchases, but I won't be pre-ordering again even it it's fantastic.
PS - Concerning the Indoc Theory. The only way I could see this being true is if it was what you originally wanted to do, began doing, and then decided to cut it out because you couldn't figure out how to do it/ran out of time. Since I don't see you guys taking this amount of heat for the ending without jumping up and saying "Hey we just ran out of time it'll be fixed up in a couple months and it will be epic." it seems pretty much a lost cause. Would have been awesome though.