Your GameCube controller would also probably work fine because you only need either L and R or ZL and ZR (can't remember which off the top of my head), and you really only need one mode of directional input. Both of those games don't use all of the 3ds' buttons or the touchscreen hardly at all, so imo, you don't need a controller. The first time I played Majora's mask on Citra, I used mouse and keyboard because I didn't own a controller. Just check the Nintendo controller layout on Google and assign your buttons according to the positions of the buttons, not their names. The advantage of using a Xbox controller is that they're cheaper and they're basically plug-and-play through XInput if you're on Windows, while still maintaining essentially all of the same buttons of the 3DS/Pro Controller, just with a different layout (for example, B on the Nintendo controllers is actually A on the Xbox ones, so you'd have to use the controller thinking not about the buttons SYMBOLS, but the buttons POSITIONS in order the get the right gameplay feel, like, if a game tells you to press B, you'd have to press A on your controller, or if tells you to press ZL, you'd have to press LT, and so on).
#NINTENDO SWITCH EMULATOR FOR MAJORAS MASK PRO#
The Pro controller has the advantage of having the same button layout as the 3DS with a circle pad pro or the New 3DS (the ones that come with a c-stick and ZL/ZR buttons), so basically what you see on the screen is exactly what you would had to press on the controller, but it can be harder to setup for overall use (I believe Citra has a DirectInput option, so maybe that wouldn't be much or a problem, but it's usually better to use XInput, and to use a Pro Controller with XInput you'd need to download some softwares and drivers).
![nintendo switch emulator for majoras mask nintendo switch emulator for majoras mask](https://img.game-news24.com/2021/10/Metroid-Dread-Is-Already-Running-On-Switch-Emulators.png)
![nintendo switch emulator for majoras mask nintendo switch emulator for majoras mask](https://www.zeldadungeon.net/wp-content/uploads/2021/10/Switch_NSOExpansionPack_N64_SCRN01_Zelda.png)
Either a Switch Pro Controller or a Xbox controller (360 or One, either works perfectly) are your best options, but you can also use the Playstation controllers or third party controllers, like the Hori or 8 Bit Do controllers.