@upjumptheboogie
I love controllers and I play with a lot of them. Heck, I just ordered two of them today just because I haven't tried them before. Unfortunately, I don't have alot of experience using the Nintendo online controllers with a raspberry pi box. While I cannot tell you specifically, I caution you when using fairly niche controllers that the user base may not have mocked up some drivers for.
You are generally safe when using simple plug and play types and also Xbox clones because those drivers have been well tested.
After using dozens upon dozens of controllers for retro gaming there are a few that I keep coming back to, but your milage may vary.
I tend to use iBuffalo controllers for NES and SNES. Unfortunately, those are absurdly expensive right now. I got several when they were $15 USD, but they are going for over $40 now.
For Playstation I usually use a Logitech F710 as I like the micro switches in the d-pad. It's kind of like a Sega style disk but with four clicky switches under it.
For Genesis/MD I will either use an iBuffalo or a Retrobit Dual-link six button controller. There are several really fancy looking Gensis/MD six button clones on Amazon, but for some reason a lot of them have trouble reading when two buttons are pressed at the same time. The Dual-links seem to not have this issue.
8bitdo is another premium option, but I personally dislike how they feel. The buttons tend to be pretty great, but the d-pads seem to have a weird springy sponge quality to them.
I've tested myself using multiple controllers in challenging sections of Contra. Oddly enough, the controller I did the best with was a standard Xbox One controller with that clicky d-pad. But the buttons on that one feel awful to mash.
Ultimately, finding a controller that feels right to you is the important part. I know a guy that can do a no death run of Ninja Gaiden NES with a wretched old Xbox 360 controller. Trying to use the d-pad on that thing raises my blood pressure. But to each their own, Good luck!