Great, informative thread! I am of the fairly common opinion that culture flipping adds a good challenge to the game, but losing a large military force is not reasonable in either pure gaming terms or in 'reality.'
Suggestion: Has anyone played call to power? Ever had a slave revolt? I think that culture flipping should use a similar concept. It would probably have to be more complicated than I make it out to be, but something like this:
Have individual citizens create rebel military units that attack the occupying military units like a barbarian horde. In other words, partisans rise up from the ranks of the people. If the partisans/rebels defeat the local garrison, then the city 'flips'.
Rather than applying the flipping formula to an entire city, tweak it a bit and apply it to each citizen (pop count) in a city. Each citizen that 'flips' adds one to rebel force. If the rebellion is put down, then that particular citizen has % chance of dying (reducing city population) or is simply quelled for a number of turns (no chance of flipping for 5 turns).
You might have several rebellions over 20 turns, but never lose the city if you have stationed a large enough garrison in the city. Similarly, a size 12 city might easily see 3-5 musket men rise up from the populace to kill the 2 cavalry garrison (or you might just lose some of your units without losing control of the city). I think this would be both more realistic and more fun.
You might end up having to station a large garrison on the border with a friendly civ just to keep the citizens from rebelling and flipping...
You could end up with defeated civilizations coming back...
I could go on and on about how this might work, but I think you can get where I am coming from with this.
I really like Civ3, but I think the culture flip idea could be enhanced to improve the game. As for someone's question earlier in the thread about jobs... I manage large-scale (10-30 programmers: 6mos-3years), custom software development (system integration) projects (not games). And no, that doesn't make my any kind of an expert, but the implication somewhere along the way that gamers shouldn't question the almighty programmers was just silly.