Well I found a tedious workaround that works for me like 99% of the time:
- Run an RA core, and as soon as the first 2 [INFO] debug lines come up on the bottom screen (the 2nd one says about it loading the retroarch config), enter the rosalina menu in Luma (D-Pad Down + L + Select), and then go to the New 3DS options at the top and disable the L2 Cache -and- lower the clock speed.
- It will then get to the normal RetroArch menu. Then, when loading a rom and picking the core, it will -re-run- the chosen core, so again, D-Pad Down + L _ Select at the first 2 [INFO] debug lines...and wait for it to load the rom/etc, and then once it's actually in-game, you can enter the rosalina menu again and re-enable the L2 cache and bump the CPU speed back up.
...now if I could find out how to get mame2003-plus working. It's marked 'experimental', but so far it keeps loading up the core for 2048 after I select a rom+core :/