I'm not going to be able to actually play this until next week, so I watched a playthrough in-between studying.
Honestly, I don't think the story is bad, but it almost completely blows it in the last five minutes. There was a lot of well-written vignettes, or at least good moments with the cast toward the end that carried the proper amount of weight, and I appreciated that. I can even accept the bleakness of the story, the contrived reasoning for the Reaper's motivations (it was never going to make sense after ME2 retconned a lot of their ME1 characterization), the deus ex machina...
I don't even mind a "sad" ending, where Shepard dies or the galaxy is screwed.
But the tone is all screwed up in the final minutes of the game. Shepard makes a big sacrifice, does one of either three (poorly explained and very similar) things, and we don't get much follow-up on what any of our choices meant. What is the point of three choices if we don't even see their repercussions?*
And then to top it all off, we cut away from the main action for some out-of-place scene of Joker flying the Normandy through the relay FOR NO REASON, only for him and the crew (how'd they even get on the ship again?) to get caught up in the mass relay explosion. And our parting image before the main credits is some weird, hopeless situation where they've crashed on the ground.
I mean... huh? We don't get some sort of epilogue for the characters? We don't see the effects of our decisions? We don't even get to see the state of the galaxy or it being rebuilt? We just see an alien jungle, and our characters are stranded on it? That's just poor storytelling... there's no catharsis there.
And then we cut to the horribly voice-acted post-credits scene, which is just whatever. It just leaves a poor taste in my mind.
It's like a song at a middle school band concert that ends off-key: it was barely competent but then that last note shits the bed.
*Oh wait. Bioware.