I think the only real gain we'd have from this is more variety of craft, which people seem to generally like a lot (including myself). However, adding two slots to the max number wouldn't change a thing by itself. You also need some sort of mechanics that makes craft design viable.
I don't have a ready system in my head, but I suppose it would involve weapon slot types, so that you wouldn't be able to load anything on any slot. Or maybe some sort of energy requirement for weapons, so that you wouldn't be able to fire 4 Plasma Beams at once without having enough power sources, for example. Or maybe there would be various sizes of weapons, some of them taking more than one slot, so you can choose between four Vulcan cannons or two Vulcan cannons and an AA-gun or two AA guns or just one big ass gun.
Therefore, allowing for 4 slots is not a feature in itself, but it's a necessary step if this system is to be introduced. Since this is a rather big project, and not exactly related to remaking X-Com games, I fully understand it's not a priority (to put it mildly). However, it could have great modding potential.
