I'm late but I just finished the game. I chose the destroy option but after watching the other endings it made fuck all difference. The ending didn't piss me off nearly as much as it seemed to piss off everyone else. The child AI thing was my only major gripe but as others have said it would have been much better if it had ended with Shepard and Anderson dying side by side.
Destroying the Mass Relays did seem like a very extreme solution but it makes sense that destroying the reapers would destroy the relays too. The relays are of reaper construction after all, if the crucible was designed to target reaper technology everything they had created would have to go too, including the citadel and relays. That being said, it still didn't make any sense that the relays were destroyed in the other two endings.
I think it's pretty obvious that Shepard was indoctrinated and/or hallucinating from when he entered the citadel onwards though. The entirety of the citadel segment felt very eerie, otherworldly and out of place. The fact that he was inside the citadel they all know and love, yet as Anderson said it was almost identical to the interior of the Collector's base suggests that it was directly influenced by Shepard's memory. Also if you actually look at the corpses they're all bald, faceless and very doll-like.
It doesn't make sense that Anderson got there in the first place. When you first wake up after the laser there's no sign of him, yet apparently he went into the conduit right behind you. He also couldn't have gotten to the platform where you meet TIM so quickly and without you seeing him, especially since there's only one path up there. Then TIM shows up literally out of nowhere. Did you notice that when Shepard shot Anderson, he barely flinched and shortly afterwards Shepard clutches his side and sees fresh blood... right in the same place he'd shot anderson?
It's possible that in this scene Anderson was a part of Shepard's subconscious trying to snap him out of it, while TIM was a reaper influence trying to confuse him and indoctrinate him further. The black lines during the conversation with TIM are a dead giveaway, and when Anderson says "you're indoctrinated!" he's clearly looking straight at Shepard, not TIM. The way TIM stands there and rants about controlling the reapers instead of going ahead and actually doing it reinforces this theory. TIM, and the child-god-AI (who just happens to look like the boy Shepard was having nightmares about) try to sway Shepard towards trying to control the reapers or trying this synthesis bullshit instead of destroying them.
At that moment Shepard was in control of the crucible and could destroy the reapers, so they tried the only option they had left: taking advantage of his altered state by confusing him and convincing him to do something totally different (maybe simply killing himself). Keep in mind that you only get the extra short scene of Shepard waking up if the "destroy" option is chosen. Also notice how the god AI claims it created the reapers, yet refers to them as "we".
Then there's that part when Hackett contacts you and Shepard begins to drag himself towards the control panel, seemingly too weak to even respond, only to fall lifeless inches away from it. ...then he ascends to a higher floor and suddenly is able to walk and talk just fine. I don't think I need to point out how fucking stupid that was. Even if everything up to that point did happen (which is definitely plausible) there's no way the God-AI thing wasn't a dream or hallucination.
Also, all three ending sequences feature the Normandy in the middle of a mass relay jump and crash landing. That's bogus because firstly why the hell is Joker off doing a mass relay jump when he was in the middle of a war just a second ago and secondly how did the crew members who were with Shepard and reportedly killed by Harbinger's laser end up back on the Normandy?
Almost nothing adds up, and the only thing we can be certain of is that Shepard probably did die. Still a pretty terrible ending though since it offers no closure whatsoever. Right now all we can do is speculate and wait for more DLC or a sequel to confirm if any of this really happened.
Or maybe I'm just thinking too much and this really is just a case of bad writing. It's 3:40AM right now so I can't imagine I'm making much sense.