I think inside cities would not be a good place to set up shop.

Cities will become death traps as things start degrading due to neglect. You have basements and tunnels that will eventually fill with water. You have pipes & sewers that are waiting to explode, you have warehouses and storage depots full of toxic chemicals, etc.

The groundwater around cities will be toxic for a long time as all sorts of things seep into the ground.

After watching the series "Life without People" I would stay far away from urban areas after about 5 years post apoc.

 

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A small town may be a good option for a large community. Water could be gathered via rainwater collection.
I remember watching an old Romero film where people had a city surrounded by walls they built that was run by a corrupt governor (that sounds familiar now that I think about it) a major city would be a death trap, though a small, low population town could be cleared out piece block by block, if there was a large enough population to clear the town out.
Otherwise settlements like Alexandria, the kingdom, hilltop and Oceanside seem to be the best.
Sanctuary was an example of trying to set up a community at a factory. The ground was too polluted to grow from, resulting in agricultural collapse.

If you were to build a mega community the best place to start would be hilltop. Build wooden walls in a motte and bailey arrangement and potentially further break the motte (large walled settlement) off into sections with fences (chain-link would be quick and easy to set up as well as shoot through) in case of an outbreak and have gates between each section with a guard posted.

As for defences barbed wire and spike pits could be used to guard areas around the walls and the path up to the gatehouses could be covered by mounted heavy machine guns with barbed wire on standby to set up kill zones in case of an invasion.
A tunnel complex could also be dug allowing people to attack potential invaders without leaving the main gates.

It would take years to build, though it would be an excellent settlement to restart civilization.