Ive never even held a fountain pen in my hand much less written with one, so, I need some guidance.
Step one: make yourself a fountain pen and start using it. Everything about them and everything you read about them and everything anyone says about them will make more sense.
I know all the guys who sell high end pens, pitch the stock nibs but why?
Because the stock nibs are hard to sell to fountain pen aficionados.
Most stock nibs write well or can be tuned to write well, but some can't. On average, upgrade nibs will write better "out of the box" - but you'll want to read up on and practice tuning, and tune them all anyway.
But really, the main reason to change the nibs without even trying the stock one is because many of the people who will pay big money for a fountain pen will turn their noses up at "kit nibs".
What nibs are preferred? Exotics offers a Heritance nib upgrade with the purchase of thier kits for only a couple bucks. Is there really that much difference?
For sellability, yes. (As noted above.)
Heritance, Bock, and JoWo are all available and are all good quality. I wouldn't rank any of them above another. As I understand it, no more Heritance nibs are going to be made, so those are coming from a fixed supply of what has already been made. That's fine for replacing stock nibs in kits, if they run out you can always switch to one of the others.
What size is more commonly used?
Depends which kits you like to make. "Junior" kits take the small/#5, "full size" kits take the large/#6. If I had to guess, I'd guess there are more pens being made for the smaller size.
I also know that there are a couple different types of fountain. Some that use a cartridge and some that use a pump. What is the difference and which is preferred and why?
Kit fountain pens are cartridge fountain pens that come with a "converter"; the converter allows it to be used with bottled inks.
Probably most fountain pen lovers prefer bottled inks most of the time, so they will use the converter. As the maker, though, you don't have to worry about that since it works either way. Just don't give the customer the crappy ink cartridge that comes with the kit. Poor ink means poor writing performance, and even though it's the ink's fault, it reflects poorly on the pen.
Hope this helps. But really, make a pen. Try the crappy ink cartridge and a good one, and try some bottled ink in the converter, so you learn the differences. Try it out with the stock nib and an upgrade nib. Play with the tuning to see how to make it write wetter or dryer. And so on. Have fun!