Currently using rocketlauncher to do all of this and bezels are the main driver for using it. I'll take the imperceivable (to me) performance hit. Since we're basically stuck with 16x9 displays at this point, bezels make use of space that would otherwise go to waste, or if used, cause the games to look distorted.
For pause, manuals, save/load slots, media, and like PanteraZombie said, having a button layout would be killer. Not sure how that could be accomplished as far as custom mapping goes, but it would be a game changer for anyone who is unfamiliar with a particular system or with your arcade setup.
Save states can be tricky, in rocketlauncher you need to send key presses, often with delays, in a specific order to save to the right slot. Some emulators are easier to set up than others, retroarch happens to be very clunky if you want anything more than 1 slot.