Top side: Capcom party, and franchises who already have, oficially, either crossed over, or featured a Capcom character - whenever a 6-buttons Power Ranger comes to Mugen, it goes here;
Bottom side: SNK party, franchises who are somehow related to SNK, and everything else in the world that is 6-buttons and fits against a CvS char.
Few exceptions for the 6-buttons rule are placed at the very last slots of each side.
(Thinking about it, I could just build up a 4-buttons exclusive roster, and move them to that. )Franchises with a big selection of characters are organized similarly to how these characters first appeared in their official games, with random slots representing the
missing characters from those franchises (so it's easy to keep up with new stuff). See the Street Fighter section? And how the KoF characters were ordered like teams? That's how clever & nitpicky I am.