Instead of planets being helpful for the player, you could make them helpful for the enemies of the player. So by controlling planets, his enemies will be less effective.

I'm just going to assume your game is in a state of "we drop the player on the map and he can go find and pew-pew enemies or he can just hang around."

Which is, if you think about it, not too bad because the player wants to find and pew-pew enemies, that's why he plays your game.

Which brings me to a score, very simply give score-values to whatever you want to motivate the player to do, and let him earn that score.

(aka bragging rights at the end of the game, if it's a multiplayer game maybe have an "ongoing" score of some sorts)

Just make sure to make clear to the player where/how to earn the most score.

The concept is not score, but progression. The player will start with a fairly restrictive deploy-able tonnage and ship count(level one hull sections are rated at one ton, level five at 32 tons, this is directly proportional to their hit points). Combined with spending tech points to unlock stuff these limits will force players to build ships for specific usage and tactics. The reason for the ship repository is for players to build a ship, send it to repository and remove it from the field so it doesn't count against the limit.

Currently the plan is to have a boss ship in each solar system and destroying that will increase the tonnage/ship count limit a bit each time.

'Instant' is probably the wrong way to describe it. The ships have 'jump power' value that grows a a speed relative to the ships engine power/mass ratio. At max power the ship can perform 2 jumps in succession, but there is a several seconds gap between triggering the jump and it actually taking place. This typically takes some time though...'tactical jumping' is meant to be a key element of the gameplay...

The problem i'm having is finding a relevant reason to make the normal concepts of territory control work here. One thing i'm starting to think is I've made the planets too plentiful to have any real value. I am also thinking i need something other then planets to occupy some of that space....but what? Stations don't really count, I have asteroid maps but that's not really the same thing.

The concept is not score, but progression.

Fine, then let the planets give progression in some form when they 're conquered.

Soon the player will stop using his strategic combat skills and just use the rewards from the planets to gain progress,

and you'll have an unbalanced game, because you added progress to a game that, if you made it well thus far, already has progress.