Which Pokémon spin-off was the first to feature 3D battles with Pokémon models?

Pokémon Stadium was the first Pokémon spin-off to feature 3D battles with Pokémon models.

Released for the Nintendo 64 in Japan in 1998, Pokémon Stadium presented battles in fully polygonal arenas rather than the sprite-based style used by the Game Boy games. It included tournament cups, rental Pokémon, and multiplayer battles.

The Japanese version originally supported Pokémon from the first-generation games through the Transfer Pak, allowing players to use compatible teams from Pokémon Red, Green, Blue, and Yellow. The international release arrived in 2000 with a somewhat different lineup and presentation.

Pokémon Colosseum and Pokémon XD later brought more story-driven 3D adventures to the Nintendo GameCube. They were not the first Pokémon games to display battles in 3D.