here's sort of a summary about what i feel is wrong with the current fort commander system, pretty much reiterating what i wrote above:
1) fc's are the
only unit in the game that doesn't need to be built, that's created out of thin air. it defies the logic of the game and the player's expectations that merely possessing a tile is enough to grant a free unit
2) fc's are essentially little more than cannon fodder by the mid-game. if you're lucky enough to control a fort early, the free experience the commander gets might be enough to give you a unit that can withstand an attack or two, but once that original fort commander is defeated, the subsequent fc's are incredibly weak and impossible to level up to a point to be effective. they just become a pointless formality after turn 200 or so, in the era of horse archers and heavy infantry.
and here's my proposals for a new system along with what i see as its main benefits:
1) the fort commander unit is removed from the game. once an enemy fort is 'occupied,' any unit can cast the 'claim fort' spell, granting the player immediate control of the tile, with a cultural boost every 10 to 25 turns (i don't have a solid grasp on the mechanics of cultural control, i defer here to an expert)
2) any archery unit (or perhaps it should be limited to a single archer unit per fort, which would make it easier for the AI) may cast the 'garrison' spell. this takes one turn to cast and grants +2 defense and +2 air attack (and guardsman?) and sets movement to 0. city garrison bonuses would apply as well, and obviously a 'leave fort' spell is also required and should also require one turn to cast.
in effect, this is how one expects a fort to function, the unit stationed in a fort is making a trade-off: it is tougher to attack and has the benefit of superior positions from which to bombard the enemy, but is unable to meet its foes head-on with out losing its bonus.
moreover, this system solves the problem of fort commanders being badly outdated by the midgame. no longer are fort commanders a base 3

unit facing off against base 6

foes, instead, a powerful defender like an arquebus or a city-garrison III crossbowman could be stationed in a strategically located fort, allowing fort-commanders to maintain combat parity through the ages.
edit: like dominicus reported, loki is extremely vulnerable right now, every time i've sent him out of my territory he gets eaten by wolves within a few turns. imo he should not get the 'winded' promotion when withdrawing