On some level the conclusion they were trying to go towards could have made a good story. I get why they wanted to destroy the Mass Relays. It might have worked for a traditional hardcore sci-fi story, which is all about catalyzing change in a setting and exploring how it plays out.

But they failed to take into account the effect that 90 hours of decision making over 5 years (if you played all three games from the beginning, like I did), learning the setting, getting to know your characters, and personally uniting the galaxy could have on your ability to enjoy that sort of ending.

An ending where your decisions made little difference, the setting is destroyed, you don't get any closure on what happens to all the characters, and you have no choice but to choose some groups or another (or homogenize them into one). And I wasn't interested in seeing an artistic depiction of loss and an exploration of the human condition against a backdrop of galactic change and disaster at that point, because I was so firmly invested in the setting and characters.

Of course, on top of the ending being fundamentally flawed at its core, they did a bad job of implementing it. Plot holes, bad pacing, unnecessary plot-twist bad guy, etc.