I've noticed this too, its annoying.
It seems that by making nearly every Civ go for a warrior rush at the start of the game, that most AI's only stick to 1-4 cities at most by around 1 AD. I personally like to get all of my cities down by at least 1000 AD, as it takes a very long time to get the infrastructure up to make the city productive. Any cities after that are often just to claim newly found strategic resources. I also think that more often than not civs either pick Tradition / Honor more often than Liberty and so this has an effect as well.
But Tradition isn't the only problem. In a game I played as Rome, America had gone Liberty and was my only neighbor to the west. I only took one city site from them, which was 4 tiles from my capitol, so it was bound to happen. Then I started expanding into Montezuma's land (who only built 2 cities and got gang DOWed the entire game by all civs on the continent.
Eventually America mounted their inevitable war, which I won after some back and forth and took only one city. There was a great city location south of them, with 3 cattle, 3 gold, river and hills. Going there would give them more resources to trade around as well as make a lot of money and science for them. I was too busy expanding into my back country to try and snatch it from them. I waited and waited, founding about 6 more cities behind my front. Then by the time I had cannons the site still wasn't claimed so I munched it up.
In that game the only AI that 'played to win' was Persia, who founded a decent number of cities. I think the emphasis on going tall and culturally is too pronounced in this game and often ends up leading to some very barren land until the Industrial Era or later. City sites, especially those that claim luxuries should all picked up mostly by the late Ren. era (unless its Ghandi of course).