Thing is it would be too complicated. Already in C3C there are four different ways to improve the defensive power of a unit sitting on a square - Fortress, Barricade, Radar tower and actually Fortifying the unit. Adding a fifth would complicate matters without adding any new decisions to be made. Consider the situation in C3C: shall I fortify the unit? Yes, if he's staying there's no reason not to. Shall I build a fortress? Of course, if my workers aren't needed more urgently elsewhere. Shall I build a barricade? Yes, with the same small caveat. Shall I cover the area with a radar tower? Yes, if I have a spare worker (or a hundred by this stage of the game). Of these four decisions, only one has any notable impact on the course of the game - and that impact is limited to losing a single worker that's of relatively little use in a defensive situation.
A fifth option would similarly be a no-brainer, unless there was some major disadvantage to it (GPT, reputation hit, unusable land), and I can't say I see a simple way to implement such a disadvantage.
Perhaps if all military works required upkeep - not in gold, but resources - it would work. You could be shown the cost of fortresses, etc by the Domestic advisor and choose how many shields to divert from each city's production. In case of a shortfall, your least-used fortresses would start to disappear. You could also choose to abandon a particular fortress if you wanted to control which ones go.
A rep hit with the nations whose borders you're fortifying could work; you'd have to choose between trying to rebuild the relationship and being safe. But personally I reckon it's too much work for too little reward.
nice idea (although a bit ripped off from el justo 
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