I agree with a lot of the people in this thread (at least I think it is what they are implying) in that the fun in mafia comes from when you feel like you can do something significant, or you have some control. There are obviously other fun elements of mafia, like strategising as a team, the social aspect, and attempting to deceive people, but having the ability to significantly manipulate things with either an actual role's power or by attaining a position of perceived power in the village or as a neutral (or however it is attained) is definitely a fun thing to experience.
In the recent games I have hosted (Chaos Mafia and Wolf Mafia) I tried to make the roles fun to play and gave everyone a role of some significance (though I admit there were a few that were not fitting this description). While I don't really recommend that everyone tries to make games like those (because they aren't really intended to be as 'serious' as some other games, in that it is difficult to gain and maintain an advantage at any point due to the sheer strength of the other roles), I have received overall good feedback from hosting these games (not without complaints, however).
The next game I plan to host (with Gmax) will hopefully be fun but serious at the same time (it is a very experimental concept). There is an element of mafia that makes it less fun that I am trying to address in the creation of this game, so if I do that successfully then the game should definitely be fun!
I have had some other ideas about how to make the 2v1 system better since it is a system intended to maximise fun (as opposed to 1v1), some of these are: make lynches target users rather than aliases in anonymous format mafia, non-anonymous partially split mafias, make the mafias much smaller than they currently are (i.e. 19 v 5 v 5 v 1 or something). I have brought some of them up before, but they all have some inherent issues and none of them received universally good feedback.
Megaman served as a decent test of having an entirely split mafia faction (were both split?), and the result of this was that the village (finally) won a big mafia. This format doesn't fit the concept of mafia though, in that it wasn't an informed minority vs an uninformed majority, but uninformed of both. I don't think this game was fair to the mafia and I wouldn't advise that this be done again, but it is still a good point of reference to find how the village can win in the large format.
Anyway, since those last two paragraphs probably don't belong in this thread without something to tie them into fun: I do think 2v1 can still be fun and there are things that haven't been tried that could potentially make it more even, but I agree that it has been done to death and that some new formats should be tried for a while. I also agree that multi-faction mafia games such as Viva and those with a mix of win conditions like MGS and We Don't Need No have good potential to increase the fun in mafia while still remaining a competitive format.