After fighting the reaper in Rannoch, Priority Earth does feel pretty underwhelming since it's basically just fighting hordes of the same enemies you fought throughout the game, I would've rather have the rannoch reaper battle take place with Harbinger, it never made sense to me that the main big bad was so underused, I chalk it up to the game getting rushed out by EA but it really feels like Harbinger was sidelined.
The indoctrination theory only ever made sense to me in parts, I don't buy that Shepard was getting indoctrinated the whole game, what has become my own head canon and what makes the ending easier to digest is that Harbinger's beam did almost fully indoctrinate Shep at the end, what he expiriences at the Citadel is real but his mind distorts it, it's why he sees Starchild as the kid that died and why the options presented to him are the wrong color, it's the final test, and only destroy is the correct choice, now how he survives is still up in the air, up until the announcement of the next game teasing his return I just choose to believe he died since it matches with my head canon and what's actually canon, but now I don't know, I suppose we'll all find out when the time comes.
For all it's worth I've come to terms with and have accepted the ending, as the familiar saying goes, it's not about the destination, but the journey. The trilogy is an amazing journey, filled with emotion, laughter, action, you name it, it's probably the closest I felt to a cast of game characters and an expirience I'll forever cherish, I can only hope the next entry in the franchise manages to capture what made Mass Effect as special as it is.