I'm not going to debate story here, I'm going to debate game design. Bear with me.
Gameplay, Story, and Audiovisual Design must all be balanced in order to present a good game. If a game is lacking on any of these aspects, it ultimately does not succeed as a game, or at least not to the extent to which it otherwise could.
The gameplay and audiovisual design of the mass effect series have always pushed a fast-paced action adventure game with a solid RPG mechanical foundation. The move to cover-based combat was to appeal to a larger demographic and to keep the same pace of the game while simultaneously reducing the size of areas. As the series has progressed, the music has gotten darker and more depressing, moving away from the optimistic ambient sounds you would hear while exploring the citadel, while still keeping the same tone for combat.
This leads to the assumption on the player's part that the final game will be dark, that defeating the reapers will be incredibly difficult, but that Shepard will ultimately win. After all, she makes a habit of surviving impossible situations, and to date had only every been placed in life-threatening situations during cutscenes - never during actual gameplay, and even then there were fake-outs.
Player expectation was that Shepard would survive - or at least have a chance of survival, as was presented in ME2. This was further reinforced by the War Assets mechanic, which mirrors the Loyalty mechanic from the second game. Loyalty ensured that the character in question would survive the suicide mission, provided the player made intelligent decisions. Likewise, there is an assumption that the accumulation of War Assets will have a meaningful impact on Shepard's chances in the final battle to retake Earth.
The fact that this is not the case defies player expectation, but more so, it invalidates player effort. After the player has invested both with their time and effort, as well as emotionally, in the preparation of the allied fleet, the fact that this results in no major change in the story betrays the trust the players had in the game mechanics. It is as if the player's weapons exploded without reason, or refused to fire, or if their powers suddenly stopped working, except on a massive scale. This does not generate tension as it was perhaps intended, this creates extreme annoyance and frustration with the game.
Bioware did something they have never done before with one of their games - create a series of endings with unavoidable character failure. Sure, Shepard may technically have succeeded, but to my knowledge never before have they ended a game in a situation where the player did not achieve a total victory. In addition, it is the only Bioware ending I know of that has the player's victory come from any source other than their character's own abilities.
Is that a valid choice to make for an ending? Yes. Does it remain within the framework of past practices? No, it does not, neither does it fit the established tone of the previous games in the series, or previous Bioware games. It does not reflect the mechanics established in itself, either, making the primary ruler of success (war assets) pointless, and the overarching markers of success (choices regarding entire species, civilizations, and the individual survival of squadmates) entirely useless.
It's up to you whether you think Bioware should rewrite the ending to Mass Effect 3, but with regards to widely accepted video game design, the game does not end in a manner befitting its gameplay, story, or audiovisual design, and does not follow the expectations that Bioware itself ingrained in fans through these means in previous games.