Thanks for the info! Much appreciated.
It's a little tricky to explain how my mind works, so I'll try to be as to-the-point as possible: basically, I organise a lot of things into patterns, sometimes subconsciously, sometimes deliberately. I chose to use a small selection of Villains in each version of the game based on how they fit into those patterns, with some chosen based on how much I like them overall.
Also, I wanted to have a few Villains act as exclusives in each version, just so I had a little something different in my roster for whichever version I wanted to play; for example, if I want to race as one of my favourite Doom Raiders, I'll play the 3DS version, and if I want to race as Stratosfear, Dragon Hunter or Mesmeralda, then the Wii U version's what I'll play. Hey, even I don't fully understand how the mind of an Aspie works!
As for the Villains I chose to unlock in each game...
SKY
Wolfgang (my favourite Sky Villain, both versions)
Cap'n Cluck (both versions)
Stratosfear (Wii U version only)
Pepper Jack (3DS version only)
LAND
Glumshanks (my favourite Land Villain, both versions)
Dragon Hunter (Wii U version only)
Chompy Mage (3DS version only)
Dr. Krankcase (3DS version only)
SEA
Golden Queen (my favourite Sea Villain, both versions)
Frightbeard (both versions)
Mesmeralda (Wii U version only)
The Gulper (3DS version only)
As for the rest, Pain-Yatta doesn't fit in the pattern, I don't really like Count Moneybone, and Spellslamzer is kind of creepy; this made it much easier to exclude them from my personal roster.