It's hard for players to manually fire jumpmissiles at the times when they would be most effective since players are usually AFK. In Era 2, autofiring at orbiting, invading fleets was often ineffectual since the tactical environment favored massive Eldritch fleets, and ships with missile protection can intercept incoming jumpmissiles when in orbit/invading. In Era 3 the situation is improved a lot but fleets can still bait citadels into expending their entire arsenal.
In persistent games, players should have the option to give a citadel one or more standing orders that dictate when jumpmissiles will get autofired. Some of these orders should produce a visible warning to other players in the form of an icon over or near the citadel; others can be ambiguous. Citadels should display their firing range by default to all players when a world of their sovereign is selected.
Citadel orders could include:
ZONE DEFENSE: Auto-fire at fleets invading the empire's worlds. This should not generate a warning icon when active and should be a default order unless deactivated. Citadels already seem to do this.
JUMP INTERCEPT: Until SRMs are implemented, citadels should get an option to automatically fire jumpmissiles at jumpship-speed fleets pathing to the empire's worlds within the citadel's zone of control. (In the original Anacreon, SRMs were a construction that destroyed jumpships passing through a sector; if they were implemented, jumpmissiles could be reserved for intercepting warp ships.) Jumpship fleets passing through a citadel's radius but not pathing to allied worlds should not be fired on, or it'll become impossible to move fleets around in big games. Jumpship Intercept should generate a warning icon when active. A potential risk is that new players could end up surrounded by citadels and unable to explore beyond that because all visible worlds are part of another player's empire and covered by citadels.
WARP INTERCEPT: Same as Jump Intercept, for starship-speed fleets. Starship Intercept should not generate a warning icon when active and should be a default order unless deactivated.
WARP EXCLUSION: Citadels automatically fire jumpmissiles at any starship-speed fleet entering its attack range, regardless of the fleet's destination. Warp Exclusion should generate a warning icon on the citadel when active. It would allow players to control chokepoints that result from nebula geometry; maybe safe conduct passes could be issued to and retracted from friendly empires. There should not be a "JUMP EXCLUSION" mission because jumpship traffic is very high. This might be computationally intensive to implement since it involves a lot of point-in-polygon checks.
PLANETARY DEFENSE/INTERCEPT: Auto-fire at any fleet invading/pathing to a specific world OF ANY SOVEREIGN. This could create all sorts of interesting scenarios with players covering nearby Mesophon hubs, nearby enemy planets, allied planets, etc. These orders should generate a warning icon on both the targeted planet and the citadel when active.
It might also be cool to have a high-tech buildable structure (maybe TL 9 or higher) that conceals or falsifies how many jumpmissiles are present on a citadel. This structure would require continuous resource input, preferably nebular resources.
Perhaps jumpmissile range could be tied to citadel TL, with higher TL citadels getting augmented range.
A logical accompaniment to citadels would be penetrators, a warp-speed unit that cannot be targeted by the citadel until it is in orbit and unable to be struck by the citadel's jumpmissiles. Penetrators would need some mechanism to either destroy jumpmissiles or prevent them from firing.