I agree with thejeff. The main reason I build forts is to protect my mages. Nothing sucks like having a whole team of sages wiped out by Call of the Wild/Winds or (worst of all!) a random unlucky event. Say, for example, that Caspar finds the deepest cave in the middle of your research lab, and then your sages all get trampled by Troglodytes....
The OP is right that fortresses aren't much good for defending chokepoints. It's ironic, but true. It's usually much easier to defend a chokepoint by purchasing a load of PD (especially if your PD is decent) and a lab, then send in a couple of mages to summon new (cheap) beasties every month. For example, if you have E2 mages, Clockwork Horrors are nasty & cheap.
Another good reason to build a fort is to maximize the income of a rich province. Any province with a high population and a good income will get a substantial boost from a fortress. After several turns, that fortress has paid for itself, and the rest of the game is pure profit.