Change forts to be static units that cost maintenance and can be upgraded, instead of one type of fort that has limited use have different types of fort:
Hill Fort: Can defend itself, +50% defence for any unit
Castle: Can bombard with trebuchets and defend itself, +75% for any unit
Cannon Star Fort: Can bombard with long range cannons and defend itself, +75% for any unit
Bunker: Can defend itself, +100% for any unit, +200% against ranged attacks
Missile Silo: Can house guided missiles and 1 nuclear missile or ICBM
Air field: Can house 4 aircraft and airlift 1 unit per turn
The main forts can defend themselves like a unit of their time, hill forts-swordsmen, castle-knight, star fort-cavalry, bunker-infantry. To all intense and purpose they would be these units with bombardment abilities but unable to move, they would cost maintenance, could be upgraded and allow a form of stacking.
I was also considering a civ iv cottage style upgrade every 10 turns for hill forts, castles and star forts as villages grow around them. After archaeology any fort that hasn't been upgraded beyond Star fort provides a culture income.
The most important aspect of this is the benefit to defenders, I believe forts should be overpowered, to make attacking harder.