Some comments on AI city locations:
I have no problem with close-together cities. I often intentionally overlap mine since I often have lots of small cities that don't grow that large anyway--3 or 4 premiums is easily enough for all but my super-cities. Doing this can prevent barbarian uprisings and/or force them to occur where you can isolate and deal with them using the same unit(s) repeatedly, and lower defense units across the board.
The AI is pretty predictable in locating its cities 4 squares apart. My two-move units (i.e. Crusaders) take one city, rest, and can ride the roads to the next city on their first move (3 squares) then attack with their second move. One more square of separation would make a big diference, as my units would either need to stage halfway or attack at 2/3 strength.
I can't EVER recall seeing the AI locate a city on a one-square wide ithsmus. These are often CRITICAL squares--a city there can be a great short-cut from one ocean to another, saving the "around the Horn" long trip. There is a reason the Panama Canal is so strategically important.