... and that is a question many authors have posed in their works... like Tennyson in "Ulysses"... but the question is not really "are our choices ultimately meaningless?" but rather "on what level are they meaningful?" To just ourselves? To ourselves and our immediate friends? To our community? We are not automatons, but neither do any of us really ever get the chance to save the world either. Certainly Shepard's choices throughout the game (regardless of the endings) made a difference to his/her crew.
As I said, I reconciled it by reverting back to the Western Christian imagery of "death and ascension" - not at the point before going up to the citadel; but at the point after the final conversation with Anderson. Why there - because that wraps the last personal relationship Shepard has in the game and because, I believe, that the choice of how to save the galaxy is something that is ultimately not ever going to be in the hands of one person. Bioware inserted the imagery at that point of Shepard looking at how much blood he/she was losing and of him/her collapsing outright while reaching for the console (still wanting to follow orders, still wanting to save the galaxy) intentionally. Because of that imagery, I see Shepard dying before he/she could finish his/her mission.
I do think that Bioware should have ended the game right there... but they felt obligated (likely because it was a game) to give some varying degree of "credit" based on some arbitrarily score in order to end it as a game and not as a book... and then they dug their hole deeper by writing the EC.
If you want a story to end like a book or a movie, you should make a book or a movie. You can get away with it in a game as well, but not if your marketing campaign screams "choices and consequences" at the highest-possible volume and the previous games in the trilogy delivered on that promise to some degree.
Speaking of what Bioware should've done, back in 2011, before we knew anything of ME3's scenario, I posted
a scenario for the end of the Reaper wars which I still think is considerably better in terms of plausibility, player involvement and lore than that which ME3 delivered. At that time, I had never thought we'd get a choice that wouldn't result in the destruction of the Reapers, but my scenario could be easily tweaked to include Control-like and Synthesis-like outcomes. The possibility of taking Control should be obvious after you've read it, and a radical-advancement scenario could result from "destroy the Reaper minds but keep their tech", which would even keep the ambiguity of the existing scenario. The benefit would've been:
(1) No Catalyst, and thus no tainting of the options by having them be the antagonist's options.
(2) No artificial drawbacks not intrinsic in the choice.
(3) Absolutely no "space magic" except what had already been established in lore.
(4) No assertion of a metaphysical dimension of sacrifice.
The only question my scenario didn't answer is "why are they doing this". I don't think this question absolutely had to be answered, though. Coming up with a believable motivation got us the organic/synthetic conflict, which didn't really work very well IMO and wasn't particularly interesting, given how often it has been addressed in SF. Not answering it would've kept the "Thing we aren't meant to know" interpretation open, and I wouldn't have liked that at all, but I can't deny it might've worked better than what we eventually got.
On a philosophical basis, I think the endings really only show us that there are issues with any way we, as humanity, might try to resolve a "universal" threat to our existence as an entire species. Ultimately, our (players) disagreements over the endings tell us that we're just not going to be able to come together enough to do so. It is a pessimistic view to be sure. Still, I don't think that any of the individual dinosaurs, even as they probably realized their species was going extinct, considered themselves to be automatons and that all their own individual choices that affected their day to day living were "meaningless." Our choices matter to ourselves and to others within our actual sphere of influence... and I do also think that message is included in the game as well. The Catalyst does indicate "You have choice, more than you know."
I think that's not where the pessimism lies. In the face of an existential threat like the Reapers, there would be no dissension about the fact that it will have to be removed as a threat. The problem in RL is rather that people tend to deny that such a threat exists until it explodes in their faces, just as people in the MEU denied the Reaper threat until it was almost too late. We may never agree about the best way to deal with such a threat, but that shouldn't make it impossible to do so nonetheless.
IMO, the true pessimism of ME3's ending choices lies in the fact that you're forced to deny one or the other of your principles,
and implement that denial on a galactic scale. It's not something I can't live with, unlike others, but it sends the message that in order to survive, we'll have to deny one or the other value we hold dear. It may or may not be true, but it is pessimistic, exactly because as you said, our morality may ultimately ne meaningless, but it's not meaningless for us. I might have appreciated such a message, as pessimistic as it is, because I actually do think that morality shouldn't be the ultimate arbiter of everything, except that the drawbacks of Synthesis and Destroy are arbitrary and not intrinsic in the decision, while Control is tainted by association. Thus, people's frequent response "We shouldn't have to do it that way".
Also, they did bring in Tennyson's "Ulysses" (albeit it was optional if you didn't pursue conversations with Ashley); and although they never do cite the ending of that poem... it does end with:
I appreciate the presence of the Ulysses quotes in the story and I agree they have application for the story as a whole, but I don't think there were put in intentionally to be a metaphor for the story. There is a distinct lack of advance planning in the trilogy. The ME team even admitted it. Things changed, and most likely they had no idea about how the trilogy was to end as late as ME2's publication date. If this were a book written by one or two authors, I might be inclined to believe in such an intention, but the ME games are collaborative works with a dozen writers or more, and - that's also very recognizable - each game was its own story first and part of a bigger whole second, and intentionally so, if only for marketing reasons. Consider the infamous line "ME3 is the best starting point".