Yeah, I just realised why the original idea sounded so bad. This would be like EVE nullsec without the dockable stations and relatively safe Player Operated Stations with their bubble shields, and without the logoff safetywarp. So basically just the gankfest.
So, like we've come across in many content related threads, we need to create a world with meaningful places and differing danger levels, with some safe havens for players to go when they can't play for a while and enough incentive to move out into the dangerous areas when they do have the time (and people). Homogenic space has to go, even in this day and age of happy rainbows and all that. I'd say that the default game mode should be friendly, or at least accomodating to players who play a couple of days per week for few hours, but that doesn't mean that they have to be able to go into the bad parts of the universe and just live there without fear. Config options for the cutthroats or more pve oriented styles shouldn't be too hard to add I think.
I think that beyond saying some sort of siege system is good idea for dealing with homebases in faction warfare it's a bit of a shot in the dark - we don't want to force everyone to hardcore pvp in default game, because that's a niche crowd just like complete carebear pure pve. I doubt there's ever going to be a consequenceless pvp in Starmade, beyond arranged arena matches and the like. At the very least you'll lose the ship and whatnot.
What we really need to start with in my opinion, is to find the reason WHY. Once we have the reason we can figure out logical triggers and mechanisms to enable full scale wars that aren't griefing first and foremost. Why do we risk our assets in war? Why do we venture into the fray? Why do we not just keep the homebase system, mine it empty and move it to next system when it's calm and evil people are offline?
Do remember that playing it safe doesn't have to be a bad option by default, just that with risk the payoffs should be greater. I haven't figured out any great ideas, basically just some stuff with better ore density or some such... maybe we could go EVE tech 2 style and have some modules require materials that are only found at any large quantities at certain areas of the galaxy. Maybe the effect modules and computers, gate modules, advanced armor... to throw around some non-essential stuff that might be the "end game" gear. Hell, maybe even some t2 power or shield modules for that extra 10-15% oomph now that we're not trying to combat gigantism with them. Or nasty, nasty t2 weapons with exponentially scaling power consumption to make them the go for modules when building small weapons. Although I guess those would end up being turret guns because of the cost.
edit: for richer areas to work as focal point of faction war, the wealth should be renewable or infinite in some way (planet mining, daily respawning asteroids or some such) to make them long term goals. /edit
Should rare minerals and blocks behind them become a thing, we'd need some credit sink too to encourage trading, but again I'm fresh out of awesome ideas. Maybe allow hiring of npc mining fleets to excavate your controlled systems and bring back minerals in large quantities but rather high price? That could be just math and some random spawns that reduce the amount if destroyed (or if the selected are has no activity, a fixed %), transaction could be done through NPC at your station or a block.