Obviously, the designers wanted to make warfare more than "build and rush." They wanted a more strategic flavor to the game. You can't simply build four warriors and conquer the nearest enemy city. The first 50 or so turns are very important to the game and require planning. If you want to go to early war, plan for it. Prioritize the leap to either Civil Service or Iron Working. Civl Service is safer since Pikeman don't require andy special resource to build, and they are nearly as strong as Swordsman.
Cities are not difficult to take once you've prepared for the siege. You can make it even more difficult by city placement. Place your city with obstacles - mountains, lakes, rivers - surrounding it as much as possible, and keep your city spacing tight for mutual defense. In that case, not only do you have to worry about the city's inherent defense, you must also worry about archers or siege units within and around the cities. That becomes huge once you reach artillery and have the three hex range.
I think that cities are perfect just the way they are. I dislike the comparisons to CiIV. I don't want a new CiIV, I want CiV.