Thanks!
Making something similar for the 3ds (be it for gba or ds games) is a lot harder, because in 3ds mode most of the ds hardware is not available. Emulating a full 2d and 3d engine costs a lot of cpu for example. The ds has a 2d engine that is an improved version of the gba one, which makes it possible to just use that with some small interventions instead of emulating it.
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I've finally made a version of the wifi branch that you can actually try out for yourself.
https://github.com/Gericom/GBARunner2/releases/tag/v20190826-172450_7ae1123
With this version you can set the master and slave DS mac addresses in the /_gba/gbarunner2.ini file (example ini in the attached zip file). Note that you shouldn't open the settings when you have set the mac addresses as they are not preserved when the settings are overwritten. Eventually this will be replaced by a proper in-game linking mechanism where you can pair with a nearby gbarunner2 instance.
The wifi linking is still far from perfect, and the results are very dependent on the game and also on the environment (noise and such that can negatively influence the wifi transmission).
I managed to get stable linking in Mario Kart Super Circuit at home with two dslites (I haven't tried with a dsi or 3ds, so it could be that using arm7dldi makes linking less reliable for example). You have to go in and out of the multiplayer link menu a couple of times on both dses before it works (for whatever reason). After that I was able to play a full race on both dses without it disconnecting. I've not tried many other games, so let me know if more games are working for you.