Well, for me, one aspect that I appreciated about Covert Action besides for what you guys have already mentioned is also the 80s clothing and references (i.e. some of the terrorist organizations were bigger in the 80s than now, the uzi is the quintessential 80s SMG), which of course at the time was totally organic because those things were still fashionable. Definitely all in all Covert Action is one of the best games in a neat elegant package I've ever seen. I suppose there'd be room for modern revision, too, as in retrospect it seems like storming the bad guys' offices is too easy and too powerful. Sid Meier I suspect gave it far and away the best potential rewards and tried to balance it with severe penalties in terms of time loss if you were captured or if you were hit, but the problem was that as a player I could generally pull it off without getting hit and it was possible to get all the clues you needed to solve the whole case from a single visit to the appropriate organization.
If I were to design a modern revision, I'd make assaulting offices a bit more complex and have a few more realistic issues to balance out how powerful it is.
Nowadays it would be possible to make assaulting more realistic since we've got all these military sim games which have made basic room clearing procedures familiar to your typical gamer, and likewise the AI could be made more dangerous and difficult to deal with. Raids could be more difficult to pull off because of a time limit on the grounds that when you bust into someone's apartment and begin mowing down dozens of people with an uzi the local police will respond, so that the player doesn't have time to check each and every file cabinet. Finally, there could be a Diplomatic Capital talley where the player can only perform so many raids before foreign governments get furious with the US government and create an international incident. Maybe the amount of Diplomatic Capital lost would be less if the player makes a clean getaway, but it would be huge if the player doesn't make it out within the time limit and ends up getting arrested by the local police. Maybe there'd be a Diplomatic Capital penalty for each foreign national killed on such a raid. Finally, maybe if the player creates too many international incidents student protestors picket the CIA office in Washington going on about the School of the Americas or some such and Max Remington is fired for being a liability.
Blade, thank you for your extremely kind offer to help me set up some Deus Ex scenarios. Creating such a scenario is something I've thought of doing on and off for a long time, so who knows, maybe we'll have the chance to work together in the future. After I get competent, I mean. Heh.