They certainly had the staff to make Pokemon Stadium and Pokemon Snap. Most 2D games in the SNES era only needed like 4 to 7 developers. It would have been fine and trivial even to pair Nintendo game artists with Pokemon developers for a true console Pokemon game. It just wasn't done. It took until the Switch to see a true console Pokemon game.
We don’t know everything about the Pokémon corporate structure in the English-speaking world. Presumably Florent Gorges is researching this as we speak. But the common theory is that when Nintendo invested in Game Freak in the early 90s to bail them out, there must have been a requirement of exclusivity for the franchise in the contract. Game Freak made games for other consoles after Pokémon, and the Pokémon cards had Windows games, but the main RPG series that’s been both only on Nintendo and only done by GF. Last year was the first time another company touched the mainline RPGs: another company did the remake of Pearl and Diamond.
Second is Game Freak proper. They have always valued a small headcount. This has been a problem consistently. They never had the staff to make a console game. They always had the same difficulty with building new ideas. And when they were forced to move to consoles with the Switch, they released their worst games yet, absolutely dispiriting games that probably soured millions of kids on the franchise.