I kind of thought the point of fortress mode was that the DGs had to destroy the fortresses, not the creeps. Otherwise it's just like destroying the citadel, only that there are more, but they are reached sooner. As for the flag capping, I thought it was interesting that the fortresses would attack you while trying to capture it. That way whoever gets that middle fortress first has an advantage. I can see that being a good or bad thing.
Personally I think it would be good if the fortresses had a TON of HP, but didn't do that much damage, and didn't have incredibly high hp regen. That way its more of a "critical point." If a demigod attacks, the other team needs to go and defend the fortress thats being attacked because it can't defend itself very well (although with massive hp it can last for a long time for the defending demigods to get to it in time). This makes it more of a demigod-a-damigod sort of gameplay.