Badger: your idea on one big skirmish map is very interesting. Unrealistic, but still interesting. And certainly well worth to implement. Question is - how?
Laser: this is going to spoil trade routes greatly, which I won't like to do.
Point is that clan system cannot actually be conquered. Or, it might be conquered, but won't fall into winners hands. So that each faction has only one home. It's like this: hostile faction gathers forces in a nearby system and launches an assault, opposed by hostile bases and NPCs and players. In addition to that, a skirmish map may exist somewhere to provide for some interesting gameplay. But it won't be directly connected to faction systems. Actually, I'm planning two entrances for each faction system: one open, one secret.
Another question is how many such systems are needed. We have a maximum of 4-5 system owning factions, maybe even less. On the other hand, there are licenses that represent over 40 factions. Very different numbers, eh? Surely we won't make faction systems for corporations. But most pirates, for example, well deserve it.
