Can you get any more specific than that?
These two links might be of interest; of course, the first one was never confirmed. Note that the second link refers to EDI surviving Destroy. That was a weird rumor running around the fanbase right after the game shipped. Nobody could ever produce a video of it, and post-EC it's wholly ruled out. The interesting thing is that Weekes takes the rumor seriously, which indicates that he really didn't know what was going on in the ending.
Sure. I am a guy who loves learning more and more about the motivations that drive people. Since I was little, I loved AI and how the importance was on it's humanity. From C-3PO being fussy and scared, to Robocop struggling with retaining his sense of self, to #5 being ALIVE I was hooked. The most important story points in Mass Effect were the motivations of the AI and Shepard's cybernetic rebirth. The Geth were an enemy that I loved to hate, and when legion showed up I fell in love with the series all over again.
So the "guardian" or starkid or whatever AI shows up. For some reason he is shaped like the little kid. That could have been an interesting cruelty, Shepard's mind being used to confuse him/her by the Evil AI reading his/her mind and using the guilt. I thought that was the setup at first. It was a shocking revelation, but one I could get behind if it was rationalized. However, Shepard just stood there listening. Being forced to make a choice between the things he had fought so hard against. Control was the Illusive Man's dream, Synthesis Saren's, and Destroy was counter to everything I had come to admire about Shepard.
In my playthrough, I saved everyone, reconciled everything. I played paragon and always attempted to rationalize unless someone forced my hand. Shepard was reason, and logic, and proof that everyone could learn to deal. Instead, Shepard just stood there without any "speech" or attempt to reason with the AI. If the AI really was just in Shepard's head it became a metaphor for his/her internal struggle with morality. I might have felt better if it was simply through discussion that Shepard convinced the guardian to do one of the 3, but not for it to demand Shepard choose. It was too like the second Matrix movie. Shepard was just the .001 probability that would break the system. Maybe it was the choices. Force your will over them (Blue), Force everyone to be the same (Green), Force your will over them again (red), or fail and someone else make the choice for you later (Clear). None of those felt like a struggle or logic and reason battle. The Guardian didn't explain logically why it was doing what it was doing. It was so obviously flawed... but there wasn't a struggle there.
Up until the guardian showed up, the game was about the struggle of free will (at least to me) and beings right to live. It was ALL about morality. I don't care if my Shepard needed to sacrifice himself to save everyone and prove a point. That's fine. But what was given simply left a bad taste in my mouth and a sad feeling years later.
Getting the whole galaxy together to fight the Robo-Cthulu, cheesy but admirable. A superweapon that comes out of nowhere (ok) but has been worked on by many species in the past (not ok). What I had hoped for, was simply arguing with the big bad and showing it through what I had accomplished that it's logic was flawed. If Shepard had just died staring out the window next to Anderson, as a simple inspiration to everyone I would have accepted it and started up another playthrough. All I considered Shepard to be was an example of how one person could be a force for good and make a difference with a ripple effect. I would have wanted to see his companions mourn him, be inspired by him, and live whatever lives they now could due to his sacrifice. That they themselves then would go on to carry that torch and be a force for reason and good.
I ended up accepting (not really choosing) Synthesis because I like machines. The Extended Cut helped me feel a little better, but still uncomfortable with forcing a homogenization. I had thought that the point was celebrating and accepting differences, not negating them. I didn't feel I had made any point to the guardian. I didn't feel that I had done anything more than pull a lever that was always there, one that I couldn't morally accept pulling. It shocked me out of the narrative, went counter to the themes I had come to respect, and was so last minute and poorly explained that I am STILL left without closure a couple of years later. The reapers won in the end to me, because I was left disappointed by a tacked on twist.
Some things that I think would have made for a better narrative. Somehow finding a way to communicate to the collective "souls" of those species powering the Reapers. In some technomystical way convincing them to rise up and fight their programming in order to stop other species from becoming what they were forced to become. Perhaps causing a Reaper civil war (like the Geth) or just the species sacrificing their immortality in order to shut themselves down.
The Reapers were a mind-numbing, incomprehensible, destructive force. They were inevitability and death and represented our fears of both. There may never be a satisfactory explanation for why they did what they did... but the one we got was less than sub-par. It was laughable if it wasn't so disappointing. Again, I like explanations and motivations, but this was the perfect time to lack one.
Probably more elaboration than expected, sorry for the wall of text. I apparently needed to get this out. Cathartic.