<note warning>Warning: Spoilers for Mass Effect and Baldur's Gate (and possibly other cultural references) ahead.</note>
Foreword: My first playthrough is female Shepard (I liked the voice) romancing Liara (I liked her personality in ME1, both Ashley and Kaidan were so …). So don't get confused when I use both “I” and “her” despite me being male.
I've just finished Mass Effect 3 (with Extended Cut DLC) and tried all of its endings. After reading up on the contents of the Extended Cut DLC I understand dissatisfaction with continuity in the original endings and the final narrations definitely shifted several thing from just being silently implied to being explicit.
Beside that (I would say more technical problem), there are few things that enraged the fans. Lack of a “happy” ending, zero influence of the previous choices and a deus ex machina approach.
I'll start with the choices. Up until the final battle for Cerberus base the Shepard's choices significantly influence who gets to stay alive and shape the galaxy. Obviously not all are shown in the final movie, but throughout the story Shepard has the chance to eradicate or marginalize almost every species in the galaxy. So after the battle is done, the resulting power balance is her choice.
Personally, after Rannoch, I've decided that I would get the quarian admiralty court-martialed (or something) for this. After I create peace with the geth in ME2 they just had to go and attack them. And to top that off, they destroy an inert geth capital ship I could have used. This obviously isn't a part of the game but I consider this identification with the hero the core part of role-playing games.
Next the deus ex machina. After reading some blog posts I felt I like was the only one who saw it coming (improbable). Maybe it's because the amount of science-fiction I've read and seen or I just have similar way of thinking as the writers but after Sovereign said in ME1: “We are each a nation - independent, free of all weakness.” I had an idea what Reapers were, that turned out to be pretty accurate.
Sovereign is kind of a bigmouth but it reveals that it is synthetic and comprised of many individuals acting as one. Borgs, anyone? However when it talks about the cycle, it is presented as something that was imposed on the Reapers, because it's inevitable. Therefore someone else came up with it.
This was elevated to almost certainty at the end of ME2. The individual Reapers are the former species of the galaxy and the cycle is a way of reproduction – they then carry traits of the harvested species. This is also hinted by Sovereign in its speech as “and experience a true rebirth”. This would be a sufficient reason to continue with the cycle, but in the end, the origin of the first Reaper was also revealed. It was a functional solution to a wrong problem by a misguided AI – this feels like a classic theme, reminds me of Isaac Asimov and the Stargate series (as I said, a classic theme).
I don't feel that this is something that was arbitrarily glued on top of the story. It rather underlines the entire theme of senseless conflict. In fact I would say that the main storyline is a cheerful alternative of the one of the Battlestar Galactica series.
At first, Shepard considers both the Reapers and the geth to be just a very determined kind of toasters (with guns). And while Shepard's opinion may evolve, many remain stuck in this mentality. This eventually leads to a choice of a peaceful solution or an utter destruction of the synthetics.
And finally the “happy” part. I personally consider the three original endings quite fitting. The one I don't really like is the fourth, added one – choosing not to act and let the cycle continue is kind of pointless. The species of the next cycle would presumably succeed by choosing one of the three options, so why let everybody get killed in this cycle.
So as I've favored peaceful solutions throughout the game I also wouldn't choose the destruction ending – though Shepard achieves the original goal by destroying the Reapers (and the geth and EDI), this is unnecessary with the other options present. However the Extended Cut adds a potentially happy part to this too, as Shepard is shown to survive the blast (this is allowed, because Buffy survived her death twice and she wasn't a cyber-enhanced soldier ).
The synthesis ending is kind of unsettling, but is it implied that Shepard becomes part of every living being in the galaxy this way. While it may seem strange to humans, it should be obvious why the Child prefers this solution – it means that its primary goal was achieved, with blurring distinction between the synthetic and the organic life, it is no longer possible for the synthetic life to destroy the organic life.
And finally my favorite ending – through taking control of the Reapers (and presumably also the Citadel) Shepard transcends mortality and (in an unusual way) survives despite being seriously wounded. This reminded me of the divine ending of the Baldur's Gate saga. In both games the protagonist is presented as ascending to immortality and leaving his love interest behind.
And in both games I consider this just an omission due to lack of imagination, because same as Forgotten Realms allow gods to have mortal avatars, the Mass Effect canon has shown that the controlling mind of a Reaper can have an avatar too – Saren was one and EDI/Eva proves that even a less technologically advanced cybernetic entity can do this and have a romantic relationship in this form.
So I would first secure my control over the remaining Reapers and withdraw them, then broadcast a message that it's me and everybody should stop shooting and finally get myself a temporary body (probably a vacant geth platform) and ship it to Normandy.
Day saved, Shepard gets the girl and also gets to be a literally immortal hero for the entire galaxy – what's not to like. Now I have at least another eight centuries to be with Liara (significant improvement over human lifespan) which I think is more than enough time to do the synthesis ending in a less violent fashion.
I think that while these available endings may seem like a sudden change of theme, they are not. All three games hinted at a bigger story. If the Reapers are synthetic, then someone must have created them. Without dealing with this, the ending would be as much incomplete and the ending of the first and second game. Someone was destroyed but it's not finished. Without revealing the origins and reasons behind the Reapers there would be a reasonable doubt that there is more of them.