I was thoroughly disappointed by the ending. I had a feeling something was amiss once you beam up to the Citadel, though. The room with the corpses, Anderson somehow making it to the terminal before you (with no other direct path there), TIM as well, etc. The entire scene with Starchild and the options given were so ludicrous and disjointed from the entire ME experience that it took me aback.
Indoctrination Theory, while not comprised of flawless logic and plot, is about the only thing that makes sense to me. The kicker is that if so, BW must've intended the true story finale to be tacked on as DLC, and to me, whether it is free or not, is an injustice to gamers. Plot-wise, an awesome twist. Execution-wise, leaving the potential scene of Shepard awakening and finishing the job off the initial game is pure consumer rape.
Generally, I don't abhor micro-transactions, DLC, etc. They can augment games, offer terrific content, etc., but it should NEVER be used to offer the final chapter of a game. It's cruel, really, if this is what they're doing.