A "paper plant" that changes the body structure, preferably in a defensive angle?
Turtle shells gives nice things to Yoshis?
Speaking of that, Yoshis that evaporate upon death would be interesting, along with statinary giant sunflower plants (both from Sunshine).
Lava needs repopulation with evil, evil things. I suggest taking a look at Yoshis Story for suggestions for wildlife. (Seeing a pattern?)
Duplighost reworking for colder biomes, along with Sirens in the darker, more evil places. As such, building a gigantic,movable door to keep the most powerful caste of the sirens kept in check is actualy sound logic.
Dragons! No, realy, they are around to the point that a few flavors are feasable. A Robotic, lung type one for the desert could be a rare threat, while the varing 'Tales could be made into above-dwelling, underground-living, and hell-unliving varients. Also, because there are now grasshoppers, you could make it so that the above-grounders all are sickened by them.
Also, if you think about it, if bowser or his kin were necromancers, it would explain how Dry Bones keep coming back up.
As such, while you might add "Displaced Dry Bones" or sumsuch as a threat in the caverns, a actual base creature would be unnessisary.