Well, I've no programming experience, but I can still help by bombing you with impossible-to-implement ideas and pestering for a release to play.
So, looking at the thread, this seems to be the standing suggestion for stats:
Muscle - determines physical damage, how much character could carry
Constitution - Resistance to illness, poison, fatigue
Coordination - determines accuracy, things like lockpicking
Intelligence - intelligence based skills, hiding your trails
Charisma - making people like you, all that
Willpower - whether your character could weather non-physical stress, especially if the game implements that status-type idea with concern/worry/fear
Perception - helps you notice things that you might normally miss (sounds and details)
I think it's missing a stat to determing things like running speed and jumping height and your natural affinity with acrobatics. I suppose you could make them a function of Strength (how strong your legs are) and Coordination (how good you are at timing your movements), if additional stats would make things too complex. Also, something to determine reflexes would probably be necessary, to determine things like movement order in a gunfight and dodging ability.
Maybe break Coordination to two stats, Agility and Dexterity? Agility would be your affinity for moving, including things like running, climbing, jumping and rolling, while Dexterity would be your ability to perform small, precise movements such as picking a lock, performing surgery or aiming a sniper rifle. Most combat would use both. Perception could perhaps be combined with intelligence or willpower. Maybe make it a function of both. How smart you are combined with how much patience you have. Also, I don't like the word "constitution", and I think "health" would be better. Assuming they're even visible to the player.
I've also had this idea for a luck stat that wouldn't measure how lucky you are, but how much luck you have left. You start with a fixed amount and you can't normally increase it, and you can permanently sacrifice a point or two to do things like perfectly succeed at any single action or evade certain death. It'd make the game less realistic and more
"Action Movie", but I think that's fine. I think the most irritating part of combat in Dwarf Fortress Adventure Mode is when a highly skilled character gets killed by a lucky shot. Would it be too much like a lives system?
As for character advancement, a problem I foresee is pacifism. Since stealth will apparently be a large part of the game, any system that requires you to kill people to get more powerful is right out. A skill based system with no concept of experience levels sounds fine, as long as there are enough opportunities to train them. LCS forces you to commit hundreds of practice murders to train up your combat skills, and that kind of kills the idea of staying hidden from the authorities. Yet on the other hand, if training skills is too easy, the flow of game gets broken. If you can safely level grind skills in your hideout with no risk, the skills become kind of pointless, as every character can get them without having to play the actual game. Make training require teachers and money? Automate the training and make it take lots of time, so that if you do it too much, you die of old age?
The kind of instanced city with areas separated by loading screens that LCS and the old Infinity Engine games have would work well here, yes. Possibly have random locations for chases and such, in addition to all the areas with interesting things in them? Back alleys, orbital motorways, stuff like that. Every time you reach an edge of an area, you have a chance to get away from your pursuers; depending on how many of them there are, how close they are, bonuses for knowing this area of the city well; and if you fail, you get tossed to a random street and get another shot at shaking them off. If there's some idea on how the persistent city areas are connected to each other, you could also get to pass through some of them while running away. Eh, maybe just go with the escape minigame LCS has.
Would a DF-style persistent city be too difficult to implement? It would make leaving your mark on the world mean something.
Okay, this post is getting kind of long, so I think I'll just click post and ramble more later.