You want the benefits for being a 'bad guy' to outweigh the benefits of being a good guy? heh...
FOOL should (and hopefully will) follow the example of the previous fallouts; 'bad' = immediate gains in the form of cash, guns, ect while 'good' = doing what's right by those in the wasteland so they dont end up hating your guts.
I suppose the Khans could be treated in the game as a tribe, with their own villages and traders. If you visit say Junktown you start off with Antipathy and low barter etc.and decide to be bad or not so bad from then onwards.I am sure the developers are going to be very careful that being bad does not end up being a greiver and ruining this game like another apocalyptic online game i have seen.