I’m using the mame core, and it works very well, but I have a strange issue: for most MAME games, it automatically detects and setups my XBox controller, and maps it quite fine (actually, X-Y and A-B are reverted, but I think it’s correct given the Retropad layout). However for those games using 6 buttons (like Street Fighter), the buttons are mapped completely different (A -> X, and even shoulder buttons are all messed up). I could rebind them per-game in the MAME options, but that’s not so nice and I would prefer to work it out of the box… what is exactly the issue here and I can I solve it?
Some of the arcade cores, such as FBA, have a core option to set the controls to ‘arcade’ instead of ‘gamepad’ and this will keep them from moving around.
The idea, though, is that with the gamepad mode it will put the buttons in sane locations. That is, Street Fighter games will have the same mapping as the SNES ports.
It would be a nice idea… if it worked properly instead of messing the buttons badly, as it does 
I’ve checked, however, and I can’t find any core option for the MAME core… where should they be?
it would be in the quick menu > options (i.e., core options) and it’s indeed not there in the mame-git core. Depending on how the button-shuffling is set up, I might be able to add the alternative, so I’ll see if it’s within my capabilities.
Be more precise, i can’t help if you don’t give examples, as far as i know, all Street Fighter and Neogeo games mapping makes sense.
It’s just a personal preference. By default, it uses the 4 front buttons and the 2 shoulders one, but I would prefer to use 4 front, right shoulder and right trigger. However if I set it up for this, it messes up very badly in other games…
Of course you can’t made something which feels nice for everyone, but an option to leave the button bindings static would be really useful.
Ok, you want to play Street Fighter games the “modern way”, yes it is personal preference, but you can do that, i added a core option a few months ago, it is called “L/R P1 gamepad scheme”, change it to “remap to R1/R2”, it won’t mess with your other cores. There is the same option for P2. NB : don’t change “control scheme” to “arcade” or this option won’t work.