My favourite games are all multiplayer, so I'd like to see that as being a prominent feature. Working with this, and the free form procedural world, I can see a few interesting ideas.
The game could go down an MMO style route, and have several active cities, or even just one, that are rotated every so often. The player would control themselves. The game play would be a sort of "killer" (
http://en.wikipedia.org/wiki/Assassin_%28game%29) style assassination game, with all the players in one city trying to kill a single other player, whilst not getting caught by the police/public/other assassins. Each player could have a base to hold up in, and would defend it with CCTV that automatically emails evidence to the police if the player gets killed, or have sentry bots, or just really hard to crack doors.
Alternatively, this could be scaled down to much smaller scales. Each player has the same objective, except they are a computer literate mob boss, and have RTS style control of their minions. Minions could be set to guard targets, earn money (robbing banks etc.), and go on missions to take down the other mob bosses. This could even be played as single player quite well, with the player trying to take down an oppressive government with aggressive raids (Fight Club style?).
Overall, I think most ideas for gameplay would go down the same route of having the city being fully fleshed out, with citizens, police, corporations and rival players/gangs (this might be achievable by having a "random gang generator", with priorities and resources randomly determined, and just randomly assigning them to being cops or an underground group, and their priorities determining whether they are 'good' or 'bad'?). Once this is done, there needs to be a modifiable system of rules determining what the player controls and what the victory conditions are. In fact, this is the only real thing that needs to be done. Oh, and of course a system to distribute them. Perhaps each month has a user created game mode as a theme?