Yeah...suffice to say I don't think the 'artistic vision' argument truly applies here. When the devs repeatedly say throughout the development cycle (even during the final stages of development) that there will be many "wildly different" endings, I think it's fairly safe to say that the "1 ending, now in 3 fun new colors!" doesn't match the vision they had for the finale - especially when they note that they had to drop a good portion of it in the eleventh hour due to gameplay issues with it - and that the presented ending itself violates their artistic vision.
As presented, the ending seems rushed and inconsistent, as if they literally ran out of time to make it. If their vision had truly planned to give the same bleak outcome regardless, then the very act of differentiating the endings (despite their overwhelming similarity) becomes counterintuitive. Ironically, I think that if they had just presented one outcome (no final choice involved) the reaction probably wouldn't have gotten as much steam as it has, as it would be very clear that what we were given was intended. However, they gave three options, which quickly became a slap in the face when their near identical nature and aftermath became apparent, and that itself points to hasty design choice: filling three possibilities with the same cinematic, which they then gave slight alterations to so as to justify the existence of the three different paths.
Were I to make an educated guess on the subject, I'd say that what we were given was originally intended to be the ending for the "Destroy" options (hence why we see more variants for that choice than any other), which were then hastily edited to make the other possibilities work when they realized they'd run out of time (the general conclusion, at least, seems to be supported by the behind the scenes commentary that has since been released) So yeah, all things considered, I don't really feel it's out of line to call them out for not holding to their own vision as it was presented to the audience.
Oh, and as to the Krogans and the Genophage: No. That was not presented as an inevitable outcome. It was feared that history would repeat itself, though much with the Rachni, the initial decision (genophage and extinction, respectively) was consistently treated as a tragic decision which many objected to (Heck, the lore itself states that the Salarians only ever intended to use the genophage as a threat and didn't expect the Turians to actually use it), and indeed one of the most significant themes underlying their respective missions was the fact that they deserved a second chance in some capacity. Despite the council berating you if you saved the Rachni in ME1 (though then again, they're angry either way), the decision proves justified in ME2, when news reports and an Asari on Ilium both make it overwhelmingly opinion that the Rachni have little interest in the hostilities the council was afraid of, and were actually quite willing to be allies.
With regards genophage, dialogue with Mordin points out that one of the main problems with the Krogan in the first place was the fact that they were introduced to the galactic community before they were ready to be a part of it, and indeed an important part of Mordin's character arc is his doubts about the genophage's ethicality and its effect in practice[footnote]While the genophage itself was designed to drop krogan population growth to pre-industrial levels, the sociological impact led the krogan to become fatalistic and self-destructive and thereby was leading them down a slow path to extinction[/footnote]. In fact, if Wrex survives Virmire, you see by Mass Effect 2 that he's actually taking steps that would ultimately lead to the Krogan becoming a viable and valuable part of galactic civilization. Could it go sour? Sure, but all the same, the series does not imply the inevitability Croshaw attributes to it.
Oh and on a final note: "Audience: Fill In Your Preferred Ending Here"? Quippy strawman, but a strawman nonetheless. That would only really hold up if the upset fans were submitting preferred endings rather than the generally expressed sentiment of "Bioware, take a mulligan on that ending"
Edit: Broke up the paragraphs a bit so it's less 'wall of text'-y.
