Ahh, sound like you are looking for a FE that saves commandline options per game. Like say you run asteroids at 640x480.
Well, on a per game basis the prefered way would to make an ini file for the game. like making an asteroid.ini file with the config stuff in. (You can make stuff like neogeo.ini, vector.ini, and a couple of others).
Basically, just take your mame.ini file and make a copy, cut out the stuff you aren't going to change, change the stuff you want to change.
My FE will support commandline options per mame exe registered with the FE. Not a per game basis as those options tend to change. That's the purpose of the ini files anyway.