Time to destroy this conversation with a Wall Post! C'mon! Bring you're imaginative genious to it's limits!
Anyways, I would personally put in gasses to be implemented as new items and 'upgrades' to different 'phases' of Engines/Reactor/Beams.
A. Let the Basic Beam not consume ammo, but have the upgraded beams require ammo to fire them so it's not so much a drag on the consumer market... we should also make ammo components and all-gas ammo components to beams (to make it somewhat a challenge, but not too much, say one in... 7 beams that require a specialized analyzeable component for an ammo). The Damage, and Range should increase (Damage should increase 10-100 points on each phase, Range should increase by 0.5k-2.0k), and the Energy Consumption, and Fire Rate should decrease (figurative of Energy Consumption, and Fire Rate: decreased by 10-50 units of energy, and 0.25-1.00 seconds). Should you run out of the required ammo component, then it'll revert to its Basic Beam.
B. Again, let's not have a complete dependancy on ore for the Basic Engines, but instead upgrade them to better phases of themselves. Now the phases (and phases would have to be... well in terms of Latin... Delta, and Omega (come up with a third upgrade name to add to the engine, Alpha, Beta, and Gamma's been taken by the Progen)) would require a component that can be drained from the vault of a player, rather than the cargo hold (if such a thing can be feasible).
The components will require all-gas and will only be ripped from looted engines from combat or ripped to lesser phases. There should be a minimum of at least 50-100,000 (level 1 to 9) credits for a phase upgrade (improve for balance) because the manufacturing terminal has to fuse in the refined gas (plus container component) with the engine. Should you run out of the required component, it will only drop to the Basic Engine's Warp Speed, Thrust, and Warp Drain, rather then HALVE it so it's lesser than the Basic Engines Warp Speed, Thrust, and Warp Drain.
Now, for the gas drain on the more advanced engines, well that will have to depend on the Warp Drain and distance traveled (can't come up with an equation at this moment, will have to leave it to you guys to decide), and subtract that much from your vault, which shouldn't be too much, or too little (I can think of 10.0k-20.0k warp distance would subtract 1 unit of the Component).
C. Reactors, again with engines, but this time recharge consumes the component rather than distance... to incorporate this into the game, I would allow the Reactor to be built with all-gas components (into container components). The reactor cap, and recharge on the phases will increase (Figuratively, Cap and Recharge: 50-2500.0 units of energy, and 25.0-150.0 recharge per second), now note, that I haven't included any active or equipped buffs... which will be explained in D..
D. Onto Buffs (Activateable, Equippable, Instants, any and all of the buffs in-game).
Equipped decrease buffs - will be lessened in the primary and secondary phases (by 10-30%), but in the tertiary it will be removed completely.
Equipped good buffs - in Primary, Secondary, and Tertiary phases will be improved (by about 10-30%).
Activateable decrease buffs - will be more lethal in primary, and secondary phases (by yet again, 10-30%), and by tertiary the main debuff will be improved (by 10-30%) and include a new debuff for your enemies to fear.
Activateable good buffs - they'll be improved (by 10-30%, my favorite numbers for some reason) on the primary, and secondary phases, on tertiary the main buff will be improved (by 10-30%), and include a new, but weaker buff than the main.
Instants - I don't exactly know if there ARE bad instants, but all of them (good or detrimental) will be improved on the primary/secondary phases (by 10-30%) and by tertiary will have a new instant or BOOST to the player/enemy, along with the main instant.
Now then, sorry for this huuuuge wall o' text, but my main point is that it's a very interesting idea that I took some thought into and this is what I came out with, something the community WON'T HAVE TO use but will be there should they so choose to, and IT WILL BE useful.
*Was going to post this earlier today, internet time ran out on me, all these... figures are just rough estimates that I came up with off the top of my head, you, Developers, should come out with a balanced solution to this, we have faith in you.
- Foreststrike