Your set is so full of uses of animals (especially with the Shapeshifters) that it is jarring to see Saprolings being used on two cards rather than tying things together a bit better by creating some cross synergy e. g. making more frogs.

The shapeshifters (usually) take the form of animals, that's why so many creatures have Animal Shapeshifter Class subtypes. This is something I somewhat regret, but was one of the first foundations I had when creating Coaxkika (a continent, not a plane). I went to far to undo it. I can't remove the shapeshifter type because it makes Coaxkika's denizens indistinguishable from the fauna. There are some cards supporting shapeshifters in the set, but not many.

I use just saprolings when I want a 1/1 plant because plant tokens are usually 0/1.

You could easily replace Shapeshifter with Human or Elf or something - aren't the classes indicators that creatures like this one aren't regular wildlife as well? I don't see the particular issue with removing Shapeshifter, though it's not actually that big of an issue keeping it either (I admit though the numbers you went with for these are a little overwhelming).

Plants can be 1/1 (compare Grovetender Druids), but then again I wasn't suggesting Plant tokens, but animals that conceivably could live between the roots of a lake-side tree. ;)

No, I made xenophobic propaganda part of Eluim's military, and Eluim has most of the common Magic races. While I never named or even outright stated the existence of Urmak, I was going for that continent to have the races absent from Eluim (there are a couple one-off cards suggesting immigration in the flavor text, and the races given don't show up elsewhere in Eluim).

I guess with the class indicators it's not confusing why one is a regular animal and one isn't. Then again, Tarkir showed loxodons and regular elephant-like creatures (the naga type at least clearly differentiates snake people from regular snakes). For what it's worth, if there was art, the shapeshifters would look like animals as depicted in stylized art from Mesoamerican cultures, which I think would be a strong visual indicator.

I'll have to read up on the world building for these sets then. I'm coming at this untroubled by previous education on the topic. :)

Have you thought about a new creature type with a shorter character count? It would bind the flavor together quite well, or so I'm assuming from just this conversation