Save core settings for resolution. No way to set rom folders for each emu though.
That works! Thanks, Palom. Remembering rom folders for each emulator should be an easy fix, but I don't expect it to get fixed as the 3DS maintainer doesn't seem to GAF. The best workaround is to point Retroarch to a single roms folder with all the system romsets in their own subfolders.
For those of you wanting to fix mednafen_pce_fast's broken aspect ratio, first open up a rom
Then open up Settings -> Video
Choose Custom Aspect Ratio 256x243 with Bilinear Filtering ON, Integer Scale OFF
With rom still loaded, go to Main Menu -> Quick Menu -> Save Core Overrides
While still in the Quick Menu, Close Content
Finally, you need to save the Configuration. Do that in Main Menu -> Configurations -> Save Current Configuration
mednafen_pce_fast should now have it's own custom video settings separate from the other emulators. When setup properly, it performs much better than TemperPCE on the n3DS, imo.