Right now I'm using four different kinds of weapon slots:
fighter weapons (subach, prometheus, etc.)
capital weapons (terran turret, fusion mortar, etc.)
flak weapons (flak, aaa beams, etc.)
beam cannons (BGreen, SRed, etc.)
I'll probably will add a few more slot types depending on how well the game supports this and will probably need to distinguish between light and heavy capital weapons or flak and aaa beams, but like in Freespace's FRED, you'll still be able to create some "unrealistic" weapon setups.
That being said, a regular singleplayer Nexus mod doesn't even allow any weapon customization, so every custom setup would need to be done through my Skirmisher tool or by editing the mission files directly, anyway. I'll include some preconfigured shiptypes sticking to the FS2 canon weapon layouts as much as possible, of course, so the player doesn't need to fiddle with that to get the Freespace look-and-feel.