This might be my first time posting on the Elemental forums, so prepare the scathing remarks!
I like the starbase comparison - but with more physical barriers on the map (rivers, mountains, the bog crawling with trolls) the area bonuses need to be reduced, if used at all, and they should mainly strategic structures that force the issue or make a chokepoint even harder to break through. All sorts of fun things could go into a fortress: Training areas, forges to upgrade weapons, research locations, breeding animals, the high tower you throw prisoners off of (for the Fallen). Maybe even economic structures, like a marketplace in a border fort where the magistrate taxes imports from your not so nice neighbor.
They need to be balanced with a significant cost though, more than what was seen for the starbases in GC 1 and 2. I've done some reading on the various knighthood orders in the Crusades, and the Templars and Hospitalars spent the equivalent cost of tens of thousands of knights and soldiers to cover the cost of building and maintaining thier fortresses, then would garrison them with small numbers of troops and local mercenaries. Maybe an extreme and annoying example to use in a game, but its something to consider.
On a side note, some sort of 'road forts' would be nice. The Romans really enjoyed building things, and they organized a very structured road control system with forts and inns along the major roads to provide security. It's be tedious to levy troops to garrison every single one, but as a road upgrade it would be interesting to add. Something like 200% of the cost of the road to lower the incidence of bandits and increase trade slightly? It might make sense for some of the larger roads in the middle of a kingdom.