Certain upgrades for ships/weapons...
For example you are able to purchase new engines, that are better or worse for certain things... Different engines different pros and cons, Different specs Could be, thrust, braking, turn speed, etc...
Upgrades for weapons that you can install on your ship, example: energy chips or w/e that help with damage for weapons or charge time. Specs could be different chips would make you fire faster but lower dmg, fire slower and increase dmg, Certain resources could be stored that would fuse with the energy of your weapon to add a particular bonus.. a vamp effect, a slowing effect, etc..
Different kinds and strengths of shields.
Green is a weak shield that takes 100% dmg(wat we currently have now),
blue can take 90% and
red can do 75-80% tweak however u wish. Optional--> A colored aura can b put around your ship, the less transparent can show how much shield u possess and color would show wat kind of "shield or armor" you have. the shields would cost accordingly to type... Also the shields could possess traits that are more efficient at absorbing energy fire vs. projectile/physical fire.
New Hardware Item:
Shield packs - these could be for emergencies that could add a specified amount of shield depending on how much you wanted to pay. Example: i pay 40k i get 1k green shield wen used. I pay 400k i would get 10k shields(notice the double price-tag for the convenience of this item) of course the blue and red would cost more.
Nuclear Fusion Generator - Would increase energy regeneration for a short duration before burning itself out due to limited fuel. This could last 15-45 seconds. A must for any captain.
Warp Fuel additive - Short duration of increased engine capacity for those quick get-a-ways for the peace hippies or the pirate who gets himself in a spot of trouble.
You could do something with
Hull Strength that could be a % less of damage you take from weapon's fire. Just looking for variety. Variety = a more complex playing system with new tactics for different ship configurations you decide to use.
Btw toonces, i like the idea of say adding or Buying an extra weapons bay for p shooters/lasers. dual p shooters or quad purple laser thingies or vice versa. Also the ability to change the spray like u can with the solar cannon. Direct, narrow spray, or medium spray. You could even add on a ships secondary ability to do a Gravitational Rotation which would spin around quickly spraying in a 360 degree radius. The bullets could have a sort of momentum carrying themselves in spirals around the ship slowly further and further away until they dissolve or explode lasting saying 30 sec or longer if needed.
For a little mix-up certain engines could give a certain charge to specific weapons or shield type. Havent really thought out these ideas thoroughly as it popped into my head as i wrote it. I think these ideas could be tweaked to fit game-play properly and would add several variations players would need to win battles, invade planets, or b a tank for the "faster high dmging low shield ships."
All these ideas are at your opinionated discretion. Obviously this is a crude explanation of my ideas which is the purpose. Tweak them for better game-play and additional ideas are welcome 
