Yeah, I'm not a big fan of the Espionage system either. Late in the game, the only 'cost' to me to running tons of missions is the amount of micromanagement I'm willing to put up with...and I thought one of the cornerstone goals of Civ4 was to eliminate tedious micro (especially REPETITIVE tedious micro!).
For example, in my last game, I had over 24000 EPs to two Civs who were merrily throwing Spies at me and blowing things up left and right. They tended to have around 300-400 points at a time (since they used them constantly). So each turn I have to go to a handful of cities and re-queue a Harbor here or a Granary there etc etc. They are only one-turn builds at that point, but its the annoying micro that sucks. Ditto for improvements being constantly blown up...With a group of workers it takes only 1 turn to restore it, but you have to find the workers, move them there and order the repair...totally pointless IMO.
IMO, most missions should be able to be run from the Espionage Screen WITHOUT the need to phyisically move hordes of little spies around the map. If I want to run Counter Espionage, dont make me move 5-6 spies around to each Civ and then wait a turn and then run the mission. That is pure tedium in the late game. Why not just let me select Counter Espionage, pick a foreign city to run it in, and give it a chance of success? It amounts to the same thing but without the micro...At the VERY least, allow an ongoing cost to make it an ongoing mission...its COMPLETELY ridiculous that I have to 'renew' it every 10 turns against each Civ!
Going back to that same game, with my 24000+ EPs (and more every turn), I could have ground every city in their empires to a halt (approx 600 to run the Foment Unhappiness and/or Poison Water Supply). I could have halted their production anywhere I wanted and I could have blown up as many of their luxuries/strategics etc as I wanted. But the 'cost' was the ridiculous amount of micro that that would have taken. So instead, I just ignored 'offensive' action altogether in the vain hopes that 24000 to 300 would give me some sort of bonus to stopping their missions. Nope. I'd catch maybe 3-4 spies a turn, but 1-2 per turn would also succeed in blowing up some pointless thing that had to be replaced manually.
Without completely overhauling the system, its always going to be a micro-intensive sub-game. But at the VERY least, they could allow DEFENSIVE missions to be run without the micro. And some better cost scaling late in the game would be nice. Its not a 'cost' to spend EPs that basically earn for free with no reprecussions for using them...ie, having more doesnt seem to earn much bonus either way. And when I can easily earn 700-1000 per turn with little or no econ investment then the cost to run missions needs to scale up too or else they become limited only to the micro (and, I suppose, the need to constantly be building spies which IS a cost, but a minor one at that stage IMO...60 hammers is trivial).
Finally, the AI seems to spend so much on Espionage (much of it utterly pointless) that it lags behind for no reason. The AIs benefit from being able to perform the required dull tedious micro, but the 'cost' for them is that they seem to OVER USE Espionage to their own detriment.
Anyways, I hope upcoming patches tweak the Espionage system dramatically. At the moment, it seems to go against everything that Civ4 was aimed at correcting.
or 
to... help them along a bit...*innocent whistle* 
deposits in the ten turns, while they're devastated. I did this to Hammurabi in my current game yesterday.
