So I realized I never put my theories on them in.
Basically, I firmly believe the Parella became the Zora. That type of extreme evolution isn't new for the series, or even the Zora in particular, since they're confirmed to have become the Rito. It's supported by the art direction requiring them to be "primitive looking" and fits, since it's a cnidarian becoming a more bony fish creature, a much more complex animal, before becoming a bird.
Kikwi...are a bit more of a stretch, but I'm in support of the theory that they became the Kokiri, who then became the Korok. It'd fit the whole Double-K forest creature thing. It'd also help to explain the Kokiri wearing green tunics: it started as a Kikwi tradition in which they wear clothing reminiscent of the hero who helped their race way back when.
Remlits likely evolved into regular cats over time, now that the land is able to be populated. Rather simple.
I'm...less optimistic about the Loftwing and Mogma, though. Loftwings are based on the shoebill, after all, which are a threatened species, so it's not unrealistic to think they may have gone extinct due to over-hunting by races that revere them less than the Skyloftians. At the very least, they're an incredibly endangered species in modern Hyrule.
And Mogma I just think are outright extinct, likely to have died in a volcanic eruption. There's no way they, say, became the Goron, since Gorons already exist in Skyward Sword. Sorry, Mogmas, you are the weakest link (heh), goodbye.