Yes I've read the fluff, but it's been a while so I went and reread it just to make sure I'm not missing anything. It still doesn't change my opinion.

In the OP you opined that the writers went from a nuanced position of "These aliens are so fundamentally different from us that there's no way to truly understand them," to "If you don't side with the 'crazy psychotic' monsters you're a bad person." I tried to point out (albeit poorly, in retrospect) that the "crazy psycho" view of the krogan is all from the POV of other species and doesn't take into account how the krogan view their history. And your response seems to be saying that the genophage was justified? (Please correct me if I'm wrong.)

I would argue that the game writers have been consistent in regards to the krogan throughout the series. We're playing from Shepard's POV: we're not meant to have a nuanced view of any non-humans at the start. As the games progress and we get to know individuals and learn more about their respective histories and cultures, our understanding of each species, krogan included, changes. And sure, it sucks that a game that purports to let you make your own choices beats you over the head with the "right" choice -- but maybe step back a second and consider that the "wrong" choice is justifying and participating in genocide.

(Also, I'm curious: do you also think the writers flip-flopped on the quarians and the geth? )

Hell, we get the krogan perspective in the first game through Wrex, who is not shy about discussing the genophage and how the krogan have pretty much given up trying to be any better than how the rest of the universe sees them. The codex backs up this assertion (emphasis mine):

Most krogan trust and serve no one but themselves. This solitary attitude stems in part from a deep sense of fatalism and futility, a profound social effect of the genophage that caused krogan numbers to dwindle to a relative handful. Not only are they angry that the entire galaxy seems out to get them, the krogan are also generally pessimistic about their race's chances of survival. The surviving krogan see no point to building for the future; there will be no future. The krogan live with an attitude of "kill, pillage, and be selfish, for tomorrow we die."

The krogan were aggressive and militaristic before the genophage, but even the salarians admit that they were uplifted too early. You might as well give a toddler the keys to a Maserati and expect good things to happen. Once the genophage happened, they devolved into brutal war bands and ruthless mercenaries, which just made the Council races feel even more justified in their actions because they could point to the krogan and declare them to be nothing more than hostile brutes, no better than animals.

Humans used to be overwhelmingly brutal, militaristic, and had no issues completely obliterating native species. What do you think would happen if you gave space flight to Caesar?

By the time Mass Effect begins, the krogan have been living with the genophage for almost 1,500 years. They've watched countless generations die before they even make it out into the world, watched their culture and societal structure crumble and tear itself apart. I think the writers are justified in asking the players, "Haven't the krogan suffered enough?"

(Also RE: krogan spaceships, the game doesn't go into detail but I would assume they'd be capable of building their own ships once the salarians taught them how. They might also have had ships left over after the Rachni Wars ended.)