About the skills. I thought about something like separating skill level into two numbers, your theoretical knowledge of it and your practical experience with it and making the former much easier to train and adding skill rust. Thinking about it more, it'd be a bitch to balance, not make very much sense in some places, and not necessarily even solve the grind problem.
Is there some kind of incentive for the player to hurry? Could we simply automate grinding? I think someone suggested this already. You could set your character to sit in his house for five years reading about lockpicks. You'd need money for things like rent and food, so you'd have to leave to rob something every now and then. And you'd need to make this kind of skill gain slower than skill gained by actually using skills "in the field" so that there is still some incentive to do the latter, but not so slow that it's completely worthless. And the character could age and eventually die, LCS style, meaning that you coulnd't just train forever with no ill effects. And maybe add some skill rust for things you go without using for a while, so that just training one thing for really long times is not good.
My suggestion for skills we need. Possibly missing some things. For the most part, I'm not sure which skills should give bonuses to each other.
Combat
melee: Individual skills for attack types? Slashing, crushing, stabbing? Or maybe item categories: knives, swords, clubs. Improvised weapons would mostly be clubs, I guess. Hit chance affected by AGI and DEX, damage by MSC.
martial arts: Sriking, kicking, wrestling? Should these even be broken into individual skills? Or should wrestling be separated to grasps, holds and throws? Eh, maybe just go with the three. For punches and kicks, skills as before. Wrestling uses the same three, but in a different way, since damage is dealt differently.
ranged: mostly firearms, but any crossbows and shit would probably use the same skill. LCS has pistols, SMGs, shotguns, rifles and flamethrowers. Is that too many skills? Where would the crossbows fall here? Eh, maybe just go with weapon size, like Funk suggested. A separate skill for full automatic sounds good too. Affected by AGI and DEX. Probably mostly DEX. It could be situational. The more time you have to aim, the more DEX matters.
throwing: This might be a subskill of "ranged", although it doesn't really have that much in common with it. I think you should be able to throw grenades with fairly little throwing skill. They're not really a precision weapon, as far as I know. Higher levels would be for things like throwing knives. Bricks would fall somewhere in between. Range affected by AGI and MSC, I'd say, and accuracy mostly by DEX.
Sciency knowledge-type skills
Medicine: For basic first aid, at least, and more depending on how sophisticated the wound system will be. INT and possibly DEX, at least for some procedures.
Chemistry: Making (and safely handling) explosives. Also acids if they come up. Identifying and manufacturing drugs and poisons would probably use both this and medicine. INT.
Computers: Do we want realistic hacking or Hollywood hacking? Are we even going to have computers? INT.
Other: I guess any "street smarts" and such would also be knowledge skills?
Mechanics and electronics
Mechanics: Not sure if there should be a generic "mechanics" skill. It'd probably give a bonus to lockpicking, at least. What else could it be used for? Repairing cars? Repairing watches? Repairing diesel generators? Is anything like that going to come up? Maybe merge this with Electronics? INT and DEX.
Electronics: This'll be needed for explosives. How detonators are put together, how to make them, how to defuse them, stuff like that. Also working with electronic locks, hotwiring cars, repairing machinery, disabling security systems and anything similar that might come up. INT and DEX.
Lockpicking: Opening locks, ranging from bicycle locks to combination locks. DEX.
Movement
I'm not sure if there should be skills for jumping, climbing, swimming and such. Technique doesn't matter that much. Your ability at those should mostly be determined by the relevant stats. A dodging skill would fall here as well, and that one would be so useful that everyone would want it. Maybe make it difficult to train? Except then we're back at grinding. Eh, maybe just go with stats.
Things missing
Driving: Probably in a LCS-style chase scene minigame. I'd suggest leaving cars static, multi-tile objects that you can't manually drive. It'd be cool to have a trunk, like in Fallout 2. Maybe entering cars, putting things in the glove compartment, stuff like that? Oh, yeah, the skill. What'd this be affected by? DEX? INT? Maybe even AGI, since that's part of the reflexes meta-attribute.
Social skills: There'd probably be a couple of these. Haggling, persuasion, stuff like that. Affected by CHA, possibly INT, maybe even WIL?
Stealth: Moving without being seen. Also knowing whether you are seen. Probably INT and AGI or DEX.
Disguise: Moving without attracting attention. And knowing when people are suspicious. INT and CHA.
Sleight-of-hand: Some kind of skill for picking pockets and doing card tricks? DEX, maybe CHA?
For lockpicking, you could make skill mostly affect how quickly you can pick the lock, not whether you can pick it. That way, you could access places with strong locks without epic-level skills, it'd just be more risky since it'd take time. And you'd still need some minimum level of skill to understand the premises of how the lock operates.
This model would leave HLT, MSC and WIL mostly useless. That's fine for HLT, at least, since it's otherwise helpful, being the stat that keeps you alive when you get hit. And muscle is for carrying capacity. I'm a bit worried about WIL, though. It'd be used for resisting pain, fear and boredom, but what else? We probably aren't going to have mind control, are we? Maybe doing anything under stress should be harder, stress here meaning anything from drug withdrawal and sleep deprivation to loud noises or an audience, and willpower would let you resist the penalties?
AGI and DEX are used a lot. Maybe too much. Perhaps we need a Perception skill to make guns and knives use different skills. Of course, they'll still be necessary for dodging. Meh.