I can see the SD adaptor playing a huge part too. Not only could you make your own maps, but with the space of SD cards you could make entire campaigns (A standard for PC strategy games) and take them over to your friends house. You could download new missions or even units (remember Cavedog's one unit a week for Total Annihilation?) onto the SD Card. The possibilities for multiplayer are almost endless. Just put in a quick and easy, but at the same time reliable and filled with options, online interface (Blizzard's Warcraft III should be the major direction to look at), and you could very well have yourself the best online console game to date.
As for N64 Wars...it was only in Japan of course, and it probably wasn't 3D. I don't think Intelligent Systems even knows how to model and program in 3D...The closest they've done is Paper Mario which is not a full 3D game. But hey, EAD can do 3D perfectly fine...Intelligent Systems doesn't have to program the game, they can stick to mission design, balancing, etc.
EDIT: As for online...yeah I don't see this huge dream of mine happening this generation. But an online Wars title with all of the above features could be easily done next time around. Oh...and then there's GBA link-up. Why not put coding on the Cube Wars disc (or whatever Wars, for the next console), that has all the stuff necessary to take Advance Wars 2 or 3 or whatever online. Link up your GBA, with cartridge inside, and then be able to take it online through the Cube Wars menu. Of course, I'm not sure if the GCN/GBA cable can handle that kind of data flow...but hey, maybe next time you could have a built in Game Boy Player, that DOESN'T turn the console into a full GBA when you use it. Retain the console's features, while playing GBA titles at the same time. I think that should be a major selling point for the next console. Take your GBA games online. After all, the thing holding back awesome multiplayer games like Super Circuit and Four Swords is the simple fact that finding 3 other dudes with link cables, GBA's, and cartridges....isn't too fun, or easy.