That could definitely be part of it. Maybe the license reqiured so many mini games or something, or required each licensed character to be featured in a game that was beneficial to their image/abilities. If so, the number of games was probably too big for one cartridge on either platform at the time (Konami was known for skimping on memory on the SNES).

I like to think they had competing development teams working on this license, one for each platform, and they got to pick back and forth what mini games they wanted. Competing development teams internally is, or was, big in Japanese companies. Look at how close we came to not getting the Game Boy because of internal development teams fighting each other to push their work over another team's efforts.