True, the idea of grouping skills isn't too bad. What if it is kinda Fable-styled where the more you use a skill, the better you get with it, while at the same time you can use experience to throw into any skill you want?
Why? What's the point of experience?
Read above, dude. Getting better in skills you only use forces you to only really be able to use those skills, unless you want to suffer a huge penalty and be really weak when switching your fighting style.
And...? So you make sure you use skills that you think you'll need and you make due with what you have. That's what a real agent would have to do after all. As part of the character creation the player will probably get to choose several skills and the character will probably already have some basic skills. There's also the possibility for the player being able to spend time practicing with a skill he thinks he might need - shooting range, practicing martial arts in a dojo, etc.
So if the player comes upon a situation that normally requires a skill the character doesn't have, it just means he needs to find a way past it using the skills he does have. That's part of role-playing. That's not to say he couldn't take a stab at using skills he hasn't mastered. A person can try almost anything and if he's normally good at most things (as an agent should be) he shouldn't be a complete failure at whatever he tries.
Creating an artificial system to allow the player to arbitrarily "buy" skills for a character, enabling him to magically become an expert in skills in which he has no prior experience is just silly IMO. Yes, that's how it's been in the past, but it's still silly. Why not innovate and use a system that actually makes sense?
< /soapbox >