There really isn't a solution.
Everything those posters suggested in impractical.
See the thing is, there isn't a cfg/ini/ctrlr file just for alternating player games. Without such an option, you are going to have to manually check all games to see if they are alternating, and manually remap in mame via the menu accordingly.
The games are supposed to be played that way. Have player 2 sit back and just trade places when you are done.