These are the instructions from the Gateway website to install the MSET exploit on the N3DS (note that you must boot into Gateway mode in sysNAND, not emuNAND):
1) Copy the Gateway 3DS ULTRA Launcher.dat to your New 3DS microSD card
2) Copy mset_<region>.cia to your New 3DS microSD card (where <region> is your console's region)
3) Copy “DevMenu.3ds” to your Gateway 3DS microSD card.
4) Boot into the Gateway menu with your preferred entrypoint (Zelda or Cubic Ninja)
5) Select the new “NVRAM INSTALL” option from the menu, proceed with installation.
6) Once installed, boot into Gateway mode and launch DevMenu.3ds from the multirom menu (press SELECT)
7) Start DevMenu and import mset_<region>.cia from your SD card.
8) Reboot console and verify you can now boot into Gateway mode with the classic System Settings DS Profile method. (Settings -> Profile -> Nintendo DS profile)
9) Enjoy! No more cartridge swapping required to use Gateway 3DS on New 3DS!
Pasta CFW and ReiNAND CFW both support the N3DS now. ReiNAND was just updated to provide support for the N3DS and has emuNAND support; however, it still requires Cubic Ninja to boot.
ReiNAND has emuNAND and region free, so it's starting to look pretty good. Gateway also supports region free, so if you have a Gateway, you can go that way too.
Yes, Gateway supports exFAT and the 3DS supports FAT32, so a 32GB internal SD and 128GB Gateway SD should work. I have not tried using a 64GB SD with my 3DS, so I'm not sure if that would work..