I would like to see a very simple fare system (enabled by smart payment systems as are being implemented) -- fare by distance. You are charged a flat rate per tenth of kilometre, according to the distance between entrance and exit points. No zones, no time-based rules, no type-of-vehicle distinctions. This would incent people to use transit efficiently, and incent the system to provide the most efficient means for moving people around.
(Obviously, if you didn't tap on and off, then you would be charged full fare, perhaps with a penalty.)