Fandom...we need to talk.
All-in-all: Bryke are decent idea guys, but not the best writers. Without peer review and peer veto, they flounder. And someone needs to sit them down for a long talk about taking legitimate issues about marginalization and colonialism and so on...and putting them at the center of villains' motivations in order to make some sort of point about "extremism" or whatever.
However! Note how none of that can at all be reasonably attributed to the S.S. Mix It Up becoming canon. If anything, I'd say that said pairing—and, really, romantic subplots in the show as a whole—suffered for it to some degree; blaming it makes about as much sense as blaming any other endgame pairing. But, nonetheless, people do seem to be claiming that the specific pairing in question somehow derailed and "ruined" the story.
Additionally? The claim that Bryke called fans who "criticized" (I'll go into that later) the pairing homophobic is spurious. In case anyone doesn't want to actually bother reading the post: the actual accusation was that people who claim that a pairing with two books' worth of subtly-interwoven 'shiptease (which is more than any other central-cast pairing got) "came out of nowhere" (and by the way: it can't have both derailed the story via excess focus and come out of nowhere; the two contradict one another) were "looking at it only through a hetero lens." In other words, heteronormativity—the presumption that two female characters who have previously shown interest in men must definitely be entirely hetero unless we're definitively told otherwise in the narrative.
Let's also not forget that overt bigotry is, in fact, as much a thing in this fandom as any other. And, regardless of what you may or may not 'ship, let's refrain from shielding that lot. (Won't even go into how a lot of what passes for "criticism" of the pairing itself comes off suspiciously coded, either.)
Whew. Got that off my chest, although I'm not sure how coherent it was. In before someone accuses me of being "hateful" or whatever.