Kaizo
Tektite
Petal Meadows is just PM64 Chapter 1 with a dragon and Keelhaul Key is just PM64 Chapter 5 with a pirate theme so I'd be hard pressed to call them unique. Pirates weren't even a new trope to Mario at that point.
I’m glad you brought up pirates, because I actually have my own theory to share that I don’t know where else to post.
So, in Super Mario RPG, there is Johnny and his band of sharks - the Bandana Reds and Bandana Blues, obviously being the pirate threat of that game. In TTYD, there is Cortez and the embers. The embers are considered to be something like spirits / ghosts of past things - considering their pirate theme and the same angry yellow eyes the Bandana Sharks have, I propose perhaps these are those same sharks post-mortem. At the very least, I feel like Johnny’s sharks have to have been heavy inspiration for these embers.