What was the best Nintendo partner that went MIA?
By MIA (missing in action), either they disappeared from making games (Skip), ceased to exist, or stopped working with Nintendo on projects (Noise). These can also include big name publishers that directly worked on Nintendo IP for some time, before stopping (like Capcom with handheld Zelda titles in the early 2000's). With that in mind, here is a short list of some MIA Nintendo partners:
Treasure - Sin & Punishment, Wario World
Noise - Custom Robo
Skip - Chibi Robo
Red Entertainment - Fossil Fighters
Vanpool - Tingle, Dillions Wild Western
AlphaDream - Mario & Luigi
Monster Games - Excite Bots/Excite Truck/Excitebike, Wii ports to 3DS
iNis - Elite Beat Agents/Osu! Takakae! Ouendan
Tose - The Legendary Starfy