Why not reward specialization? And I don't just mean of the city, but of the tile. Four sets of grouped together low end housing in a tile should give a small bonus to population added by each, just like four markets grouped together should give a small bonus to the money earned by each and four sets of grouped together high end housing should give a prestige bonus. It shouldn't be a particularly large bonus, but big enough to encourage the player, instead of willy nilly scattering his improvements across the landscape, to cluster them together in one location within a city thus creating residential districts, merchant districts, science districts, ect and so forth, which could further be the location of various types of quests and activities.
I think it would give a more real feel to your cities, especially if the quest/event system were drawn into the nature of the districts that you as the player created.
