What version of Desmume do you use? 0.96? The only version I found and compiled that worked nice with Wi-Fi was 0.96 but this version is so slow compared to 0.97.
Did you tried to battle against friends with Friend Codes? I tried to do that with a friend but when we were about to battle the WFC...
btw i feel this a good time to remind you guys that sea of thieves was made by rare, who also made DKC1-3 and DK64, alongside banjo kazooie and conker's bad fur day