Yeah that RealFort mod is nice and definitely thought out a bit, but the only use I can think of for forts in my games is to build them to protect resources. That simple (and seemingly obvious) implementation would bring forts into the strategy of building a successful civilization in Civ IV. The ZOC would just be a sweet extra.
I've never built a fort in Civ IV yet, but if they fix it, I'll definitely invest the time and effort to get them into place. I'd hope the AI will atleast try to do the same. Boy that would make capturing enemy resources a very interesting challenge!
I would suggest:
1. Obviously have got to be able to build them over developed resources.
2. Zone of Control
3. Because of ZOC, cannot build forts on adjacent squares relative to each other. This would go a long ways to prevent the spamming of forts all over the place. Especially since some resources tend to be clumped together. You have to really think about where that fort is going to go.
4. RealFort mod - which is basically unit promotions specific to forts.
5. An extra possibility of stopping sabotage of the square on which they are directly located (NOT squares in ZOC, very important for game balance).
edit: Put some more thought into this....
6. They can only be built on a tile that has some kind of improvement already in place, even if it's just a road.
7. Some logical exclusions should stay in place, for example, you can't build a fort where a windmill is without destroying the windmill (or vice versa).
8. Can't ever build a fort outside of your cultural borders, so it's treated just like any other resource improvement in this case.
9. You can build a fort adjacent to an enemy fort as long as you are inside your cultural borders. If your culture overtakes an enemy fort, then this is the one exception to the adjacent rule *or* that fort is destroyed as well as having its units expelled. The latter doesn't seem realistic, but might be necessary for game balance.
10. Along the same lines as #9, if you militarily capture an enemy fort adjacent to your culturally bounded fort, you destroy that fort.