As I see it, the main games are more 'traditional', in a sense, and generally have more refined ideas than side games. Although that is a laughable term, seeing as BZP Mafia is quite different from the mafia of other forums from what I have seen. Perhaps we should try a traditional forum mafia sometime.
Side games are generally much more willing to change things around with ideas that are not so refined, much more ambitious. It would also seem that some people would rather host side games than main games, or the other way around for other people.
There were also Point series of Mafia, which seemed to either be training for new hosts with a smaller amount of players or people experimenting with ideas.
Having a side game for every main game also allows people who missed sign-ups for one or the other to be part of a mafia game whereas if there were no side game, they would have to wait. It also placates the many people who want to host much faster. I don't really mind having both or all three, as long as they are all sufficiently different from each other. What matters the most, in any case, seeing as this is the games & trivia forum, is that the games are fun, IMO. Logic, as we all know, was banished from the G&T forum long ago by a nameless, enigmatic wizard who is said to have brought mafia to BZPower.