@jplank Glad you got it sorted out.
I did test with my old SN30 - turns out a firmware update makes it able to switch modes - and pairing always worked (either in D-Input or X-Input mode). I couldn't point my finger on it, but the connect mode might have been the culprit - interfering with a the scan used for pairing by the BT module.
Its always the last thing. Must have had some kind of hardware issue. reflashing my ssd has solved any issues. no idea what the original cause was. Some random little glitch is my guess. I was trying to avoid reflashing because of how far along I was in config, but backed it up and restoring it now that the controllers are all working. Thanks for attempting to help me h2805270, i appreciate it.
I tested the same controller setup with a pi3A so I have confirmed that the controllers are working properly. It seems to be an issue with the pi0w as both I have on hand had the same problem. I will rethink my genesis focused build to leverage the 8bitdo mod30s on a pi3A instead.
The question is - do I leverage a Genesis cartridge as the case or some sweet colorful nes carts I just picked up. I would need a label for the genesis cart. Let me know if anyone knows of a place to get a custom genesis cart label (preferably that fits on an EA sized game).
@mitu I did remove all connected / paired devices several times. I did also reset ES_input file. Nothing worked. Always when I try to pair it, it gives me error message, that device is already registered. The same with udev.