I'm sorry for not posting on here in quite some time. I finished Mass Effect 3 a couple of months ago and am actively in support of the fanbase's dissatisfaction with the ending. Here are some of my thoughts on the matter.
I think the "meaning" behind each choice is only figurative. The player never sees the results of the choices, and all three yield the exact same end to the game. There's essentially only one ending, and the different color is the only substantial variant with each choice. I suppose you can consider this to be in the "lack of closure" category of complaints, but I see this as a separate issue. They should've at least tried to have the cutscenes be marginally different instead of identical save for the color. In other words, there's only one ending to the game despite the appearance of three different outcomes. It's like the same chocolate bar with a different colored-rapping.
I think destroy is the only legitimate option because that has been the goal throughout the entire series. Making the goal change in the last scene of the game goes against everything the previous titles and Mass Effect 3 stood for. That is a major fault in my opinion. Here's my take on each ending:
Control: This doesn't make practical sense since Shepard convinced the Illusive Man to shoot himself or shot him regardless because of his ideas being wrong. Pursuing his ideas after killing him is not in Shepard's nature. I find choosing this option to be siding with the antagonist's idea, which Shepard should not do under any circumstances as a story component. As for the results of this choice, the Reapers are still intact, presumably under Shepard's control somehow. I suppose in theory he could use them to help rebuild Earth and fly to other star systems to retrieve supplies for people as the relays have been destroyed. However, no one knows that he is controlling the Reapers, so that wouldn't work. I don't really see any positive outcome from this choice, and taking into account how his home planet was decimated, as well as Garrus and Liara's home planets, I don't believe Shepard should choose that option because he is betraying what they fought for.
Synthesis: This is implied to be the best option because it is unlocked last in terms of EMS. Like I said before, how the hell does that EMP change all organisms' genetic codes and DNA? Everyone now is half metallic? How does that create peace? How will that stop people from creating new synthetics? It won't. Plus, the Reapers are neither dead nor are they under Shepard's control. Do they retreat into Dark Space? What makes everyone so sure they won't keep purging the galaxy anyway? I also don't like how the Catalyst seems to sway the player into choosing this option. Doesn't that mar the idea of player choice when the game indirectly recommends an option for you?
Destroy: The best option because it is consistent with the goal of the entire series. That goal cannot be altered in the final scene of the trilogy, and that alone makes it the best option. However, why is it painted as the worst option with the highest level of negative consequence (in theory) with the deaths of all synthetics? Like I previously stated, the game doesn't specify what synthetic means. Yes, the Geth are synthetic, but what about the Quarians and people with biotic implants? Do they count? Also, why the hell does Shepard continue to walk into the explosion rather than shoot at it from a safe distance? That's one of the worst instances of lack of narrative coherence I've ever seen. Shepard should not be dead as a result of the option, even though he/she supposedly is.
Now for that special scene after the destroy option. Why would the game imply that synthesis is the best ending when only the destroy ending contains the scene? I think the developers should've committed either to the fact that Shepard ludicrously died or that he/she comes out walking so the audience knows Shepard made it through. This scene felt cheap, and it doesn't even let the audience know whether he is alive from that. All it contains his Shepard taking the breath. At least show him breathing for a couple of seconds or him clenching his fist to represent that he is alive. It's stupid to include a scene that just adds more ambiguity in an ending already filled with too much.The surrounding looks like street rubble unfortunately as opposed to the metallic tubing of the destroy option, which is evidence of the Indoctrination Theory. There's really no good reason why that is: Either the Indoctrination Theory is true, which would be awful, or Bioware just got lazy, which isn't exactly a great thought either.
Another main problem I have is with the Mass Effect Relays being destroyed. Aside from going against the idea of Mass Effect 3 in terms of uniting the galaxy, I think this severely downgrades any of the choices because it presents a much more dire and immediate problem for the story. All of my questions pertaining to the endings must be put on hold because the galaxy is in such a terrible state that they don't really matter. The relays are out, which means the ships cannot go and get resources from other systems. Earth is in ruins, and everyone will presumably starve to death.
I know there's been a plot hole involving how Earth is still intact when the relay exploded, because in the Arrival DLC when that happened the entire system was wiped out. This time it was presumably different because it was blown up internally from the EMP blast somehow. It sounds skeptical, but I'm willing to buy that. It doesn't concern me. What does concern me is the fact that the EMP blast, which isn't apparently supposed to affect inanimate objects, sent the Normandy out of control and caused the ship to maroon on the planet. The same thing must've happened to the other thousands/millions of ships stranded in that system. So apparently their ships all spiraled out of control, possibly crashing into Earth or the Moon or another planet, or a just in a limp state in space. Either way they have no control over their ships. Whether this is a temporary setback is unknown, but if that is true then millions of people in those ships will die of either starvation or from crashing.
Do you see where I'm getting at here? The choices don't really matter because everyone is screwed anyway. That's what it really comes down to here. Hell, it might've even been better to have the Earth incinerated by choosing the Destroy option with low EMS. At least the people wouldn't suffer for weeks on end without food. It seems to me that any other choice aside from low destroy option merely postpones the inevitable deaths of millions for a few months at best.
I could go on longer, but I think I've already crammed in too much information into one response. I'm sure I represent many fans who are displeased with the ending in saying that these are all legitimate issues and more than enough to justify the hate towards the ending. It's saddening that there is really no "fix" for this whole thing. Even if they created a new ending that everyone loves, it wouldn't have the same level of impact compared to it being in the game the first time. It's called a first impression, or initial feeling, after viewing the ending of any piece of entertainment medium, and that's something we can't erase from our memories. I still think changing the ending for a better one and the fans overlooking the current one for the changed one is the best option, but unfortunately it won't be nearly as fulfilling as we'd hope for.