I've had a fascination with the villages in Minecraft. I usually build my own village from scratch via gold apples and potions, or patronize a village I've come across. But that is all they are: villages. A population of typically no more than a couple dozen or so.
I would imagine a proper city in Minecraft to be roughly the size of a small biome (think ice spikes-sized, no more than a few dozen chunks). The city would be well developed, defended (walls, guards/golemns, an armory, whatever) with several amenities and services available to the people. Inns, taverns, shops, apothecaries, and the such.
But such prosperity tempts danger, with bandits stalking the streets to pilfer your valuables. Who knows what they may drop should you manage to shake them down. Or perhaps something more sinister lurks...
As for what other trials and treasures these citadels of civilization might hold, I'd like to leave that open to interpretation/suggestion (within reason of course). I just want to get my idea down on paper for others to bounce ideas around.
tl;dr: a tiny biome dedicated to village-like structures with unique dangers to balance what would otherwise be op.