It ignored any set of conventional writing tropes and basic writing guidelines in order to introduce something that was previously unexplained. Which may sounds like a good thing, but the reason why they are tropes in the first place is because they work.
Mass Effect followed a pretty conventional writing style. Introduction, rising action, climax, descending action, resolution (or something like that, writing class was a while ago for me). And also, it's worth adding that whatever direction they decided to take, the one thing Bioware needed to do was to actually have a epilogue tying up all the character's loose ends, which it neglected.
There's examples of the stories that can go neglect this basic writing style, but generally there's an underlying point to all of it, and it's usually much better done. But you absolutely do not do it to a conventional trilogy like Mass Effect.
What happened in Mass Effect 3, was that it sort of got to descending action, and then followed it up with another out of the blue thing that really just disrupted whatever was suppose to be going on. It made no sense, was extremely complicated, and the whole time that the little shit was explaining how it worked you couldn't help but ask either "why? That makes no sense" or "no, because I just disproved that point throughout the game".
And relying on the stupid little "this is just how it is" without adequately backing it... anyways.
I think what happened was that they wanted to have the ending go out with a bang, and they wanted it to leave an impression on you. But the only impression it left with everyone was "Why did you end it in the worst possible way", and to me personally, "That was fucking stupid", because in all fairness, it was. We expected a conventional ending. We were left with more questions than answers. It wasn't just that it was a sad ending. It was a sad ending for no reason.
It didn't work for the Matrix, it's sure as shit not gonna work for this game.
When people say that it effectively ruined the entire series for them, they aren't lying. When there's something that is that profoundly negative and nonsensical manages to have an outcry from nearly every person who played your game, you should probably take that as a sign that you fucked up.