Personally I agree with Azuria. Strictly speaking it should be based on canon.
However, Danbooru being what it is, even though it isn't very likely, Mokou/Mystia is fine the way it is now. So, even though it doesn't fit my definition, some consideration can be given to how popular it is. Besides, I don't think anyone wants to go through and mark 20-30 pages of Mokou/Mystia.
Some leeway should be given the other way, too. Just because a pairing like Meiling/Marisa, Meiling/Reimu or Sanae/Utsuho isn't that popular or common, none are unlikely by any stretch. Or, as I recall, one picture that was marked as unlikely despite the two being from the same house. Not that it'll ever stop someone who thinks otherwise or doesn't know any better.
Frankly, "a fanon couple that is drawn often enough is a likely couple" gives fans justification for any shitty and unlikely pairing they want, but that's for another day.
TLDR time. Personally speaking, canon determines what is and isn't an unlikely pairing. Normally those are called crack pairings in fandom and crack pairings are, by definition, unlikely. That's the way I see it and always took the pool to mean.
As to what makes a couple likely, that depends on who you ask. Coming into contact in canon or at least having the chance to do so is a start, along with possible frequency of encounters, and having something in common.
That's a problem I have with Flandre/Koishi and Remilia/Satori. Both are popular in their own right, but they would never even have a chance to meet anyway. And as I mentioned before, Mokou/Mystia very likely wouldn't work due to a few different things.
As for Mokou/Wriggle, I forgot that firefly may not translate over there, but they're at least in the same game, which is more than most crack pairings get.
On post #551558, the shoujo-y style, the pink glow around them... it all gives the impression of them being a couple.