I think one of the biggest problem with the endings, and why they are so unsatisfying, is because they seriously break the rule of "show, don't tell." You have this Guardian come out of nowhere, and tell you that organic life is (for some reason) destined to kill synthetic life. The issue with this is that we've seen through the game that organic life and synthetic life don't necessarily be at odds. They can even co-exist peacefully. In fact, Shepard can actively broker a peace between a synthetic species (Geth) and organics (the Quorian). This is also disregarding the fact that EDI, an AI, never had any conflict with organics, and always tried to help them and "her crew." So, we've SEEN through the game that organics can get along with synthetics, so being TOLD that they must ALWAYS end in conflict and that synthetics are destined to end organic life...well, that rings as false.
What's even worse is that the only synthetics we've seen trying to destroy organics...are the Reapers, and the Geth who follow the Reapers. So once more, being told, "No wait, those guys you've been fighting the whole time...THEY'RE ACTUALLY THE GOOD GUYS! They're trying to SAVE organic life!" Well...that's a pretty hard pill to swallow. The series didn't set up synthetics vs. organics. The series set up Reapers vs. ~everyone who isn't a Reaper!~
Also, it makes me a little uncomfortable that the ending of ME3 just seems to take at face value the fact that synthetics vs. organics is always a thing, will always be a thing (as long as they're not all merged into one big magic being), and that synthetics will ALWAYS wipe out organic life form. I find some unfortunate implications with this. Not only is it stupidly Luddite, but the fact is that a big theme in ME2 is, "do synthetic beings 'count' as lifeforms?" And it comes overwhelmingly in favor of the idea that, "yes, yes they DO count." Legion and EDI are shown to be more than just mere machines. They have feelings. They are a part of Shepard's crew. They fight for Shepard. They fight for organic life.
So, to have the game say, "Yes, these do count as a species," and then have the series say, "And they will ALWAYS take this sort of action NO MATTER WHAT," well...that's just dumb.
Think if the game came to the conclusion that, "Humans will ALWAYS destroy any other species that they come into contact with, because it is part of their nature." I'm pretty sure people would have a problem with it. Because it is a dumb statement. It would be even worse if we still had Shepard (a human) going around trying to save ALL life on the galaxy. Just like we can have EDI and Legion (synthetics) fighting FOR the organics. We see synthetics fighting for organics, so hearing that they will always be in conflict and ALL synthetics will ALWAYS take a certain destructive coarse of action...well, within the constraints of the series it seems a little...racist? Speciesist? Stupidly closed-minded? I don't know, but whatever it is, it rubs me the wrong way.
Plus, doesn't the Guardian invalidate his own logic by...you know...being a synthetic? If synthetics always try to kill organic life, why would he be trying to save ANY organic life? Wouldn't he just try to end it all?
Also, weren't the Reapers setting everyone up to be culled? It seems like, by keeping around the Mass Relays they are ensuring that technology will always evolve the same way (because, you know, that's how technology work), which ends with organics creating synthetics and the Reapers coming in and eating everything. This seems like a rigged deck to me.
Anyways, I don't have any problem with "bittersweet" endings, or even "dark" endings. I kind of figured from the beginning of the third game that Shepard was going to have to sacrifice herself, and I even figured that the Earth was probably doomed. The problem with the endings wasn't that Shepard didn't punch every Reaper in the face to death, then jump into the Normandy hot-tub and pop a bottle of Cristal.
No, the problem with the endings is that they are bad storytelling. They blatantly violate the "show, don't tell," rule to their detriment by consistently showing us one thing, and at the end telling us another (and any time you have to have an "Explainer" character at the end, your writing is suspect. Hitchcock only got away with it because he's freaking Hitchcock."). It violates one of the larger thematic elements of the last game ("Synthetics are people to! People who will ALWAYS KILL YOU."). AND, it violates its own internal logic ("Synthetic life will always destroy ALL organic life! Disregard the fact that I, a synthetic, am telling you this to try to save organic life. And the fact that Reapers, synthetics, were apparently created to save organic life.").
I'm not upset that the endings weren't happy. I wasn't expecting a happy ending. I'm just upset that the endings were stupid.
You can have a satisfying conclusion to a story and still have questions. Not everything needs to tie up into a neat little bow. In fact, frequently, "and everyone lived happily ever after" is more of an asspull than anything else. But endings DO need to fit the rest of the story. And these...don't.
Shepard has always been the patron freaking saint of self-determination. Saren says that Reapers are fated to destroy the galaxy, the only way to save everyone is to join them, Shepard says "FU," and blows Sovereign away. ~Everyone~ in ME2 says, "This is a suicide mission! You're all fated to die!" Shepard says, "FU," and lives through it, even potentially bringing his/her entire squad out the other side with him. This is the character that, against all odds, can bring together every race of the galaxy to fight a unified threat. So, you're telling me that this character, who has always done things the way he/she saw fit...this character is just going to lie down and take it when "The Guardian" says, "The galaxy is fated to end this way...because I say so!"
That just goes completely against the rest of the series! It goes completely against Shepard's character.
Look, I can understand destroying the Mass Relays. That way, the galaxy can finally be free from the Reaper influence and can have self-determination for the first time in...forever. That, thematically, makes sense. But the rest of the endings are based on a premise that I just can't believe within the context of the story. I just can't believe, from what I've seen in the games, that synthetic life will ~always~ rise up against organics. Nobody can say that they ~must~ or ~must not~ do anything, because the game pretty much determines that synthetics do have free will, and saying that any creature with free will is then ~fated~ to act a certain way just...doesn't add up.