They're an odd thing to define. By raw statistics, literally every ship in this series is rare because none of them have a significant following - but that's not taking into account how popular they are within the fandom, relative to everything else.
Eribo, for an easy example, absolutely decimates everything else in terms of content, but if we compare it to every other ship in existence, its popularity doesn't stack up at all, despite it being the only possible ship that could theoretically stand a chance.
So, to determine what a Failtopia rarepair really is, let's establish three tiers of ship popularity, under the cut:
There are five primary ships in Failtopia, the big threes of both seasons in a Venn diagram. Failica and Roseyawn from S1, Eribo and Marion from S2, and Lanchi from both. Definitely not rarepairs, comparatively, because there is/was a large volume of people in the fandom on board with these.
Under every imaginable category are the proships I won't bother naming because obviously. Some of these weren't made with harmful intentions, a lot of character ages weren't confirmed back in the day, but they remain inconsiderable by every metric.
Everything in-between these two categories counts as a rarepair in my book. The fandom's too small to get much of any content out for these, and no, one person making a bunch of content for it doesn't count, most rare pairs originate from exactly that. It's an intensely respectable grind, but it doesn't change popularity statistics really.
Now, for the actual point of this post: Showing appreciation for some of them. There's too many to cover them all, so to avoid showing my personal biases, I put them all in a wheel (based on this spreadsheet of all the ship names) and spun it five times, and below, are my thoughts on each of the five I got. That's a lie, I rerolled a few times because I got too many repeated characters, but still.
Friendboat (Failboat/Friend):
Never been a big fan of C!Fail ships, but as I've said before, this is the one I'd pick if I had to. There's definitely something here, Failboat being a wandering loser who keeps getting pushed into danger by forces he doesn't understand, with a Cleric behind him who knows those forces far better than him. Not to mention their dynamics with Hank, where he cast aside Friend and left them in disarray, while Failboat feels immense empathy for him even after his attempt on his life. Healing and light motifs all around, I like it.
Yawnbo (Pirahnyawn/Bo):
Okay, I know no-one ships this, but it theoretically exists, so it has to be on the list, and now I have to talk about it. Roseyawn was undoubtedly a thing in S1, that was never subtle, but they were also never a good relationship, with Yawn feeding into Rose's ego too much, and Rose never having the confidence to call Yawn out on his bullshit. Bo, on the other hand, has way less of an ego problem, but also has a lot more confidence. She could easily keep him in check, and who knows? Maybe he can learn a thing or two from her energy.
Chiko (Deko/Chi):
I think this is the most concentrated sunshine/grump dynamic you could possibly find in this fandom. Deko's whole character is being pummelled into the ground with trauma and depression, and folding as a result, while Chi transforms her just-as-tragic life into something magical, something enjoyable, with the flick of a wand, and a stupid grin on her face Deko would never match. But as we see in canon, they have a shared fondness for destruction inside them, and they would enable that side of each other so hard if they started dating. That's a fun dynamic.
Frose (Rose/Friend):
Therapy. This pairing would be one pure, concentrated therapy session. Both of them have been so fucked up by succumbing to divine forces, they've both had their personalities warped to places they never thought they were capable of, and neither of them fully hold up once their images are shattered - but at least they'd have someone else who went through much the same. Someone else who committed unimaginable sins in a simple attempt to please everyone, and who may be able to set them on a path to heal.
Boob (Simple Bob/Bo):
That is, in fact, the most logical combination of their names, nothing to see there. As for real talk, I think there's a demonic motif that could be played around with here. Bob dedicated his life to demon hunting, taking out genuine monsters who made the peaceful world of Miitopia dangerous for pretty much the first time, and Bo? She was literally an assassin, with access to sharp fans and hidden bombs. But not only was Mar her target, the man behind the demons Bob originally fought, but she's developed far past her dangerous state and embraced her demonhood as something to protect Miitopia with. Seeing each others' positions would bring about complicated feelings on either side, and that does pique my intrigue.