I remember last game I played in Civ2. I quickly expanded and conquered two of my neighbors. Then I decided I wanted to sit back and go for a space race victory. The problem is the AI kept attacking me and I kept conquering them. The problem was that, each time I'd defeat them, they had less and less chance of beating me. It got the point where I had no problem defeating enemies on all sides. Simply put, since expansion had no limits, my strength increased exponentially. It ended up being frustrating because I had to constrain myself. I would defeat enemy units, but not take their cities. It was the only way to avoid a conquest victory.
The point is that the game is set up to offer balanced options. If you want to expand militarily, that's fine. More cities gives you more unit support, greater access to resources, and more production. But it's designed to give diminishing returns in order to allow those with different play styles to still be competitive. But, in the end, a large civilization with a good infrastructure will always beat a small civilization with good infrastructure. The game still rewards expansion if you do it right.
It was a problem in Civ II. If you could choke off a good bit of land and backfill you dominated. Though really I do the same in Civ IV a lot. The problem though was the AI was stupid and attacked you one at a time.
I guess the problem though is that there really is only one best way to play and that isn't fun. If you go play a game with all human players the focus is always on military. No one builds 5 cities and tries to space race it. You can't.
To make Civ fun for those who don't want to have 40+ cities and 300 units you have to limit it.