A very old idea that I had was if a faction was trying to take over a town, you would need to successfully complete some number of attack missions (number depending on players we have)... basically making that progress bar go up within a certain time period (hours, days, weeks, months?).
Economy seems like a very natural solution for this... if a city is under siege or blockade, they need a few things: food, water (water possibly being provided by the location, by being built around a river or reservoir), building materials, and ammunition (possibly manufacturable from raw materials if it's an industrial city). Building materials for repairs could be cannibalized from non-defensive structures (such as private dwellings), which is a tradeoff, since the economy of that city would take longer to recover by doing so (less demand for luxury goods when you don't even have a place to live).
The defending nation, its allies, or neutral entrepreneurial pilots could bring these through supply missions: you start on an edge of the map (with the town being in roughly the center of a square map, or the opposite edge of an elongated map, depending on how many approach routes there are), and must simply make it through the blockade and deliver supplies to the town. Ideally you make it through alive, though you could crash into the town -- depending on the severity, some to all of your supplies may get destroyed, and if you crash into anything besides empty ground, you'd be doing damage to your own town. The AI will naturally try to do this, but they'd be easy to shoot down (and with too many losses, they may just give up on the town).
The attackers could have at least three attack mission types:
assault: destroy as much as possible, and harass the town (this weakens the town's economic contribution to its controlling nation), and may disable that town as a spawn point until rebuilt.
siege: attempting to break through defenses and deliver ground forces to occupy; the ground battle could be implied, with troops just being another deliverable resource -- if enough attackers land safely for long enough (all hull damage after the armor is destroyed could injure or kill troops), then the town will be overwhelmed.
blockade: simply starving the town out -- staying out of range of their defensive armaments, but preventing resources from being delivered in.
Towns could have a meter indicating defensive strength. If defensive strength is high when an enemy action begins, a portion of allied ships (relative to defensive strength) could opt to spawn by the town; if defensive strength is low, most allied ships would have to spawn far away from the town (giving the attackers time to attack the town without much resistance). If the defenders win a match, defensive strength increases; otherwise, it decreases, with damage to a town counting in favor of the attackers winning. Towns could also have a state, such as the state of being attacked or not -- a player mission would always be needed to change the state to something worse, but the state could continue to have a dampened effect on the town between missions.
Scouting missions could also exist: the strength meters of enemy raiders along a trade route could only be fully known if you manage to explore enough of a given map without dying too much, for example.
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As far as economy goes, even if it's not fully dynamic, I find an important part of keeping that aspect from getting stale is to have supply and demand (not just the amount of, but also the types of resources) gradually shift over time as a form of economic climate; it could change in response to events (or a major event could randomize the economic nature of a town drastically), but in general it would be predictable over the course of a week or two (if you play constantly and are good at noticing trends, it'll usually be predictable), but will give something for periodically returning players to do, however artificial (or not) the economy is in terms of the underlying mechanics; sometimes the easy way out can be good enough and still sufficiently interesting.
I rather like the idea of a faction's ships being community-distributable across the world map, including AI ships -- players could jump into battles wherever their own or AI ships have been positioned, with force strengths relative to where the faction has its concentration of ships. Those ships would take a while to position (for offense or defense), and trade routes take a while to adjust or open up. Players could maneuver their own ships from map to map (or much more slowly have them auto-navigate themselves [such as when logged out] across the world map), but may have a negligible contribution to force strength. This can also help to make an otherwise static economy quite dynamic -- since the community controls ship distribution, they can block established trade routes, or form new ones that were previously too risky to lone-wolf.
I imagine smaller ships would have considerably less cargo capacity then large ships -- a 1v5 single-player blockade run mission could be manageable in a squid, but would have little value.
