S tier: Cave Story + (Switch) Cave Story (DSi Ware.), Cave Story (3DS eShop)
A tier: Cave Story (free ware), Cave Story + (PC)
B tier: Cave Story 3D
C tier: Cave Story (Wii Ware patched)
D tier: Cave Story (Wii Ware unpatched)
I remember in a interview, Tyrone mentioned the game was devolved in about 9 months, and for the first chunk they didn’t have 3Ds dev kits... so the game was fighting a downhill battle from the beginning.
All I really know about is Credits Wii
My best guess is that Cave Story Wii Ware started out as a almost exact copy of Cave Story (Free Ware), but then they decided to add stuff like the updated ost and graphics, challenges etc. Just a theory however