I registered an account to simply state this: It would be a damn shame to waste all that extra geometry with scripted missions.
Basically, I hope to god it's a sandbox game with more depth than carjacking and assault. So many buildings in GTA 4, and you can't even go into 10 of them. None with any potential for exploration. I understand that what my mind produces for ideas is polluted by Dwarf Fortress (a game of unenviable complexity) but I'm really hoping for some serious depth and open-endedness, here.
To illustrate, an example: You have a story mission blinking, but you need some extra money for new gear and stuff, since you just barely pulled off the last one. You decide that a little industrial espionage could be profitable, so you pull open the business news on your in-game web browser. Company X is in dire straits after Company Y managed to get a product identical to theirs to market barely a month after it was announced. Turnabout is fair play, so you steal a recently-announced project and sell it to Company X to buy new gear for the next story mission.
That type of Uplink-style freelancing, not even with the BBS requesting black ops, would give endless replayability (for me and those like me, I guess). I can't stress how much I enjoyed Uplink, simply due to the openness of it. Granted, there was only one right way to do everything, and there wasn't much wiggle room in much of it, but they're computers. Shades of gray don't go over well in binary. This gives a lot more freedom.
Say the Hard-on-crime Mayor is coming up for re-election. He'll channel more money into the police and put your teams in greater risk if he's elected, so you put together a team to sabotage his campaign. Kidnap / harass / replace his speechwriter, declare him legally dead, get him investigated for corruption, funnel his money into the campaign trust of the guy who advocates education instead. After the election is successfully rigged, the time between a security breach and police intervention is lengthened. Enough of this sort of thing, and maybe the police won't trouble your agents at all.
Or maybe you're tired of the private security firms putting the kibosh on your ops. Hire away their agents and get intel on all the buildings that they work for. Better yet, let him keep his job and put him on the payroll as a sleeper agent / spy, taking down the security firm from the inside. Do this enough, and you'll have a whole troupe of expert agents and a whole slew of buildings that don't have any real security anymore.
I realize that these would be difficult to implement in a large-scale production, even harder with a limited workforce, and you guys have both problems in spades. I understand how much sway my thoughts and opinions have, but you can't say that what I described is impossible, or wouldn't make a damn impressive game.