Good morning.
So, it's decided. Urban Fantasy.
I was thinking about the backstory since it was pretty obvious it's going to be UF. My idea is that there are many planes which are moving through the void all the time and one plane got dangerously close to ours and from time to time "leaks" releasing magical energy, various creatures and artifacts. There would be three main factions: a faction that is officially a private defense company, but knows about what is happening, a group of scientists-magicians that want to understand the other planes and often do so in morally questionable ways and a group of sorcerers that came from the other plane and want to see this plane destroyed. The government and the civilians are oblivious to what is going on.
The player could be in any of these organizations (even the "evil" one), but it would be more for backstory than gameplay advantages. The player could also be a civilian who found out what is happening and has his own goals. Also or acting as a team PVP isn't forced, but possible and needs a serious RP reason. You can't suddenly go insane and attack everyone, but if you were insane in the backstory, you can. But you can't go sane again.
Now, since the main questions are answered:
Character advancement: Point build system? Class system? Advantages/disadvantages system decided on character creation? Build system (as in there might be a build with +1 to marksmanship, but -1 to magic)? Something else? Personally, I like advantages/disadvantages systems. It's easy to bring abilities that make sense in the backstory to the actual game.
Crafting: Should I bother with it? Why should the player bother with it? How do you craft?
The fun part - if you want to, you can make up your own creatures/technology/factions/etc. and if I like it, I will put it in.