When Lucas changes Star Wars, it derails characterization, adds nothing new and decreases the quality of the film. When Ridley Scott changes Blade Runner it makes it more coherent, a better viewing experience and better conveys the story in ways the original cut failed.
When Bethesda changes the ending to Fallout 3, it adds new content, adds choices that improve the narrative coherence of the scene and additional gameplay elements (ie, main quest continuation) that better mesh with that which has come before.
When changes are made that run counter to the themes, narrative conventions, lore, characterization or even gameplay that has come before, it's generally considered a bad thing because it damages the integrity of the art as a whole. By that same logic, when a sequence in a narrative has these same problems, people have a similar reaction because the coherence of the experience is damaged by those moments. In another story, the ending we got could fit in perfectly, if it maintained the tone, themes, central conflict and gameplay precedents of what came before. It would mesh with the whole, and people would be OK with it. By that same merit, someone could write a scene where two bounty hunters sit at a table and the protagonist fires after his assailant. It's not inherently bad (though it is a bit dumb n principle) but it didn't work in the narrative it was inserted into.
This is the case with ME3's ending - the ending itself feels out of place for the same reason Lucas' changes feel out of place in Star Wars, so the rationale behind asking for them to be changed is in fact the same one as asking for Star Wars to remain the same. We want something narratively coherent, thematically consistent and in keeping with the gameplay precedents set up earlier.
People talk a log about "artistic integrity" without giving a lot of thought to what the term means, when really, it's not about the art never changing - if it was, that went out the window as soon as From Ashes was discovered, it's about art making sense and remaining true to a specific vision the whole way through. That's why From Ashes reinforces the game's artistic integrity, instead of damaging it - Javik is an important part of the lore, and a consistant, coherent addition to the game in which he fits seamlessly. If instead we got say, Blasto the Hanar Spectre as a squadmate, that would be awesome, but it would be tonally jarring and undermine the themes of the game, damaging it's integrity. In Star Wars, the original cut had artistic integrity because the themes and storyline were consistent from start to finish. It's integrity was damaged by Lucas' changes, while Mass Effect 3, had artistic integrity (which did kind of get iffy around ME2, but the game was internally consistent enough to let that slide), but the ending itself damages the artistic integrity of the series as a whole by betraying it's core principles.
A lot of people will argue the ending served to make the point that no matter what you do in life, in the end you die and all your choices are moot, but those people fail to comprehend the game as a whole. EDI's character arc involved her discovering the vales and nature of organic life, and how it creates purpose through its legacy beyond its own lifespan. Shepard's role in the entire series has been one of self-actuallization and the triumph of free will over inevitability. The core narrative of Mass Effect deals with the legacy of the Protheans and the fact that its last survivors were able to slow the eternal cycle of the reapers by giving their own lives. The theme most often reinforced by the gameplay is one of a single person influencing vast outcomes simply through an unwillignness to sit by and let things happen - even the citadel side quests and supporting different participants of an argument reinforce the theme that what you do has consequences. The ending cannot tell us what we do doesn't matter because the rest of the game tells us it does. That internal consistency is the broken integrity of the series as a coherent piece of art. It does not belong in Mass Effect, and that above all is why the ending fails.
Also, are you really surprised that after three games about how much your choices matter and how you have to fight to defend that which you hold dear some people took that to heart? It's a testament to just how well Bioware built this series that people refuse to let it end like this.