Some misunderstanding in this thread. First, someone said they "don't like the way linux looks". Linux at its core is just a command line. There are a lot of desktop environments that sit on top of Linux. Each of those DEs have skins. The options here are effectively limitless. Retropie comes with LXDE desktop environment.
Aspect ratios are configurable. My emulators all start up letterboxed (on the sides) 4:3. Just go in to the UI and select settings -> Video -> Aspect ratio -> Core provided. Save changes. You can also do this in the config files if you prefer.
Also, you shouldn't be having to type endless lines of code to do things. Maybe a handful of configs to get you going but then you should be able to save changes via the UIs for the emulators and they should stick from session to session.
NeoGeo needs a bios file in the directory with the roms.
....
Okay, I have been tinkering with Linux and BSD for years so I have a jump here. But I still run Windows on most of my daily work machines... I'm not a Linux defender. My first arcade project was a Porta Pi (just a few weeks ago). You can download his image here if you prefer:
http://www.retrobuiltgames.com/porta-pi-arcade-help/porta-pi-software-os-download/It already has all the major emulators loaded. If you follow his wiring diagrams from his Porta PI assembly manual then most everything will already be bound correctly in the emulators for you.
NES, SNES, Genesis and GBA all run flawlessly for me. 0.375b roms have some quirks but a lot of the legacy stuff runs just fine. Several games have audio issues though, some minor. Some major. My main complaint at the moment is I can't hide MAME games from the UI. Everything else I have sussed out. Took some tweaking here and there but like anything, make a punch list and work through it a quirk at a time.