I agree with the eRe4s3r, only I think it should be changed up a bit:
All units produced from that specific planet has an additional boost to its stats:Speed, Attack, Health, and Sheilds.
All structures on that planet gain added bonuses in the same manner, but resource buildings like metal harversters get an increase in resource output.
Each level gained from experience points unlocks upgrades for ships and structures from that planet can be available. This alows the player to customize his fleet to his wishes. For example, there could be an upgrade that gives the units produced from that planet a 5% chance of delflecting enemy fire, or maybe an upgrade that allows the units to regenerate over a slow period of time.
Now moving on to starships, they should work like an HQ, where they get stat boosts, and upgrades like increased multi-shots.