Jumpships are overpowered and everyone knows it. Players can build huge Eldritch fleets that can attack anywhere in the galaxy in minutes and then retreat to an impregnable capital protected by starfrigates or to an inaccessible nebula pocket so that nobody can retaliate when the player is AFK.
Upon deployment, every jumpship fleet should get a generous "jump radius" (a couple hundred light years?) centered on the planet that the fleet is created from. The fleet should have unlimited freedom to move at jump speed within this radius. However, the fleet shouldn't be able to leave this jump radius under its own power AT ALL! Jumpships should still be able to be grouped into fleets with capital ships (and maybe also gunships?) and moved around the map normally at starship speed. A fleet merger function would be helpful, as right now merging fleets requires transfer to a planet and redeployment. To move a jumpfleet to a more distant area, it should have to be attached to a starship escort and then detached when the combined fleet is orbiting a planet near where the jumpfleet will be operating. The planet where a jumpship fleet gets deployed out of a mixed fleet becomes that jumpfleet's new jump radius center. This planet does not need to be controlled by the player, it just informs the area of space which the jumpfleet can operate.
Explorers would not be subject to radius restrictions.
Mandatory starship escorts when conducting campaigns far away from controlled space would dictate that once a player moves a jumpfleet into a distant region of space, they are committing that fleet to remain nearby for a while and can't pull it back to an impregnable position immediately. If the player wants to withdraw the jumpfleet to a safe point, they can either A) park the jumpfleet on a defended planet that they already control within the jump radius, B) move it into a nebula (or out of a nebula), i.e., move it to somewhere the enemy can't easily deploy gunships, or C) reattach the jumpfleet to a starship fleet within range and evacuate. A starship fleet should be forced to remain immobile for a couple of hours after jumpships get attached to it, so that nearby gunships or jumpships under an active enemy player can get a chance to attack the marauding fleet before it can flee the area. Mixed fleets immobilized by a jumpship merger that are preparing to depart should get a special icon on the map for other players, including a visible departure timer.
Jump radiuses would fix jumpship combat by making it a little more difficult both to rapidly assemble giant jumpfleets and to keep them out of harm's way once in use. Jumpships would still be very effective and probably would remain the primary offensive units, but combined arms would become critical to keeping them alive- when fighting a distant enemy, a player would need to bring along a strong starship wing to defend their jumpships against gunship counterattack. Jumpmissiles would also be more useful if the only way to move jumpfleets long distance was at starship speed.
When deploying jumpships stationed at a non-yards world (i.e. creating a new fleet) or when merging two jumpfleets that have different jump radius center points, the new fleet should get put on multihour movement cooldown and be recentered on the planet where the fleets merged. This will prevent players from placing fleets at the edges of one anothers' jump radii in a way that allows rallying and moving large jumpfleets faster than would normally be permissible, and create a trade-off for parking all jumpships on a fortress world. Owned jumpship yards and sector capitals under F&M could allow deployment without penalty. It might make sense to prohibit transfer of jumpships to and from non-yards planets that are outside of a capital's control radius for similar reasons.
Under this system nebula pockets would become extremely hot properties since they could serve as remote bases that players could operate jumpships out of without gunships being able to counterattack them. Empires would need to be much more wary about colonizing planets near or within nebulas if they're unable to operate ramjet yards inside said nebulas. This would be compounded by the poor performance of the Hammerhead and Manta against basic jumpships - it shouldn't be too easy to defend nebulas.