Yeah it sucks that Nintendo always does direct compatibility without any benifits that are possible.
Technically it would not have been that big a problem to let the 3DS use WPA2 in DS mode. I.e. a bit of firmware running "around" the DS mode could repackage the packages with the better encryption or methods like that.
Hmm when I think about it, depending on how the 3DS hardware works in DS mode, maybe something like this could be done in homebrew when the 3DS is hacked. There is not enough public knowledge about the inner workings of the 3DS at the moment, but it is possible something like that could be done a software.