Dolphin-Version: The latest development build is usually recommended for all hardware configurations, unless there is known critical regression (usually never). https://dolphin-emu.org/download/
Game Settings: You can set specific emulator settings per game: https://forums.dolphin-emu.org/Thread-unofficial-howto-using-gameini-settings-per-game
Controller Setup: You probably have to do them yourself, but not for every game. You can save and switch between them. Usually you set up a few profiles for games that are controlled similar in some way (e.g. New Super Mario Bros. and Donkey Kong Country Returns)
Game Settings: You can set specific emulator settings per game: https://forums.dolphin-emu.org/Thread-unofficial-howto-using-gameini-settings-per-game
Controller Setup: You probably have to do them yourself, but not for every game. You can save and switch between them. Usually you set up a few profiles for games that are controlled similar in some way (e.g. New Super Mario Bros. and Donkey Kong Country Returns)