While there is nothing wrong with a flintlock, it does take a lot more special considerations/learning to make the rifle shoot. Percussion caps I would always suggest to new shooters. Later, when you are comfortable with the percussion cap rifle, then a flintlock would be the next step. A lot of the stuff you learn as a percussion cap shooter will help you later when you go into flintlocks.
ALTHOUGH - if you want a real challenge, a flintlock would be a way to go and really make you work to be a proficient with a traditional rifle.
One more question along this vein. With the traditional gun would I be better served with actual black powder like GOEX or is a modern sub going to shoot as well? I know the Hunter has a faster twist than most traditionally styled guns so I was unsurewhat would be best.
If your shooting a percussion cap Pyrodex RS will work just fine for you. If you're shooting a Flintlock then yes, go to a black powder like Goex. One thing to mention about Goex, it goes off "easier" then Pyrodex. I mean, it has a lower flash temperature so it fires very easy. Also Goex is a very consistant powder and usually provides some outstanding accuracy.