The problem with a skill system is that it encourages bad behavior. It encourages fighters to wear crappy armor so they get hit so that healers can keep casting healing spells to raise their healing skill.
It encourages fighters to weild crappy weapons to raise their weapons skill.
One solution, is to make every fight a challenge. That way if a player tries to use crappy gear to get more skill boostage they die.
Another way would be for easy encounters to get more challenging over time. Let's say a player tries to improve it's skills against a rat. The rat warlord might hear the lengthy battle and charge over there to take advantage of a weakened player.
Another way would not be a time limit but a time penalty. If the user decides to spend time taking advantage of the skill system, the monsters begin to get tougher, the gear gets more expensive, etc.
I think the best way would be to always make sure that the monsters are challenging. I know you said that you wanted to appeal to "casual" style players too.
One way would be instead of a difficulty setting you could have difficulty options. You could have level-scaled monsters clicked on or off. Time penalties clicked on or off. Breakable gear on or off.
Now one thing to remember is risk versus reward. In a lot of games if you do the easy settings you get no risk but all the rewards(you get to experience the entire story and gameplay experience).
Rewards can be online high scores, a special secret ending, etc.
