It'd just be the Yakuza in Japan, though you could go back to the older styled GTA and have missions for specific criminal groups, like maybe you could go with the Yakuza and help them keep territory, or aid the Russians or Triads who are trying to break in on Yakuza business.
Moreover, the destruction of buses of nuns MUST return.
Oh what the hell, remake GTA2 in 3D graphics with more of a story kthnx.