Well, I have an idea that might help introduce an additional game element.
ie: Guild Wars (Not the psuedo mmo)
Basically, Guilds not only afford you whatever bonuses and uu's you are going to put in, but they also allow you to conduct something like a "Trade War."
So, you get Guild X and it has as a benefit, a UU, imagined something like a "Corporate Raider" that is invisible to most other units, except Recon (especially asssasins) and other UUs in it class (The UUs of other Guilds). Crossing borders with the unit is not an Act of War.
The unit has very limited sight distance and can't take advantage of terrain movement mods, so you can't use it to romp around unknown territory. But, when placed in another Civ's city that ALSO has a Guild, the unit leaches gold, stealing a portion of the trade benefits the city reaps from its own Guild. The counter to such a unit is either another Guild's UU or an Assassin/Recon unit. Give the UU and atk/def of 4 or so and terrain bonuses, just to keep low recon units (Scouts) from easily taking them out. You could also impose a limit on such UUs, perhaps one per Guild constructed in the hosting Civ's cities? (Would keep this unit from being spammed.)
The units could be blocked from going into another's territory using either a Civ's Worldspell, like the Elohim's, or a civic like Theocracy (or whatever it is that prevents the spread of other religions.) Alternatively, you could add a Wonder or a National that blocks such units from a city or the entire Civ.
The problem is I don't know if the AI could use such units/guilds. Basically, it's reintroducing a unit that was in one of the earlier Civ incarnations. Forget which one, atm. There's also a little bit more of turn-by-turn overhead calcs the computer has to do every turn for each of these Guild UUs in play and it already has to do a great deal in that area.
The benefit? It gives the player another game element to play with - Land Pirates (as opposed to the Hidden Nationality merchant pirate units.. whatever they're called.
). It's not particularly strong and isn't supposed to be, but it could go well with a player's game if they're pushing for a non-combat victory and need more revenue. The point there is to provide those who are choosing that course a more "active" game by giving them some units to move around tactically, instead of just constantly hitting "Turn."