Please make them stock matches. Please.
Three tournaments: 1v1 items, whatever settings the players choose are randomly assigned, 1v1 more traditional battle rules, and 2v2, with some kind of rules of some sort.
The game can hold 64 friend codes, so a 64 man system would probably be best.
Let players choose their partners, of course, but randomly assign the next one. Give players a 24 hour window for their matches, so basically one a day. You can make the bracket and have one whole tier of matches going all at the same time, but it may be a good idea to avoid having the tournaments all at the same time. Start with the generic, any level, any item one, and only allow starting characters, if you ask me, and have it some time soon, IMO.
The next one should be 2v2, and the last should be the traditional-style one.