Its not all that big of a deal... unless you odn't have a joystick on a control panel. This makes it a real pain.
As long as you have two buttons, it's easy. In mame, remap UI_left and UI_right to any two buttons. Using the ctrlr file is better than the in-game remapping, IMO. For example, remap UI left to "left or key_1" and UI right to "right or key_ctrl", so you could do the joysick left-right or player 1 start - player 1 button 1.
I have to switch button A to O and button B to K on my spinner control panel. (I could do it left and right... but O and K does just fine also)
You can do it that way too, but it takes more steps. You have to remap mame this way too, so you could skip switching the encoder step if you just remap mame's UI left & UI right.
Agreed... I was thinking of making some dedicated panels, but the fact that I need left and right pretty much screws up that idea.
I think it'd be ok if analog movement registered an ok as well. Every panel is going to have a trackball, spinner or yoke/wheel if it doesn't have a joystick. Heck even lightguns would work.... shoot the left side then shoot the right.
Yes, the problem is it won't work with the relative analog movements (aka mouse-type inputs)
if you don't have two buttons. However I can't see many dedicated CPs without at least one start button and one action button, or two start buttons. This covers the golf games, supersprint/offroad (2+ players), and marble madness (2 player) fine. A single trackball only CP, or a single spinner CP, if made for trackball/spinner games in general will have enough buttons, too. You only run into problems if you do, for example, and one player marble madness only CP.
Absolute analog inputs work fine (remapping to UI left/right might be needed). Heck, in theory lightguns will work if you enable lightguns and remap correctly. (But probably need to edit file by hand, with the way mame looks at remapping to an analog input.) Can't test it though, since my CRT doesn't work anymore: I'm stuck with LCD only.

(I frown 'cause I don't have
both types; the LCD is okay for most stuff, but I miss my CRT for the stuff it's better at.)