I think these should be divided into two categories:
Attributes which are unchanging or very slow to change.
Skills which are changing or quick to change.
A key should be that you want to strive for "average". The extremes of both skills and attributes should have benefits and drawbacks, but in general the ideal prisoner should be Mr. Average.
Stats:
Strength - Raw physical power and fortitude. High strength makes them less prone to injury and more able to do physical work while being more dangerous and difficult to subdue and causing more damage to other inmates/facilities/guards. Low strength are easier to control but less able to do manual labor and more prone to injury.
Intelligence - Wits and smarts. High intelligence allows them to gain skills faster and tend to get into less trouble overall (they know how to work the system). Downside is that the smarter inmates can plan bigger crimes. The amount of trouble they get into WHEN they do it is much worse then a dumber inmate. While a dumb inmate might just punch someone, a smart inmate might orchestrate a riot to cover a break out. Low intelligence means simple crimes that are easy to catch, but they tend to get in trouble more, for example wandering outside of their zones because they "forgot" which zone they are. Also slower skill progression.
Aggression - Determines their violence levels. Highly aggressive individuals tend to cause more physical violence, and get into more trouble overall but they can take care of themselves and are less likely to be attacked. Low aggressive inmates don't get into physical violence as much (though they might be drug users or thieves or escape artists and still cause trouble) but also tend to get picked on the most. When an inmate decides to go stabbing, it goes straight for the weak so the user has to actively protect these people more.
Skills are learnable items and trades like:
Cooking - Better cooks lead to better food. Low cooking is bad food but too high cooking could mean they intentionally poison other inmates.
Law - Better understanding of the law. Low legal understanding means more trouble and higher levels mean fewer crimes but really high levels could get you sued! Better have a lawyer handy
Machinery - Better machinery means faster productivity in the shop. Low machinery can lead to industrial accidents while too high machinery will have them custom crafting dangerous weapons and items.
Physical - Better physical skills mean better manual labor. Low physical skills are weak and uncoordinated. Too high though and they'll go Bruce Lee on your guards and bust out bare fisted.
To learn skills I'm thinking they can learn them several ways:
1) On the job - Assign an inmate to cook or break rocks and they'll be better at it. I don't think Legal will ever have a job training as it's a special one. This should be the fastest way for them to grow.
2) Library - books and magazines for a medium rate of learning, modified by intelligence.
3) Personal Study - working out or correspondances from their cell. Slow but they can do it without needing facilities.
I think a nice side effect is that having high skill training, despite making them potentially more difficult to manage and keep in their cell, should reduce them from coming back. Developing trade skills could be a tool for the eventual "rehabilitation" expansion where you evolve from just housing criminals to trying to help criminals.
