Great thread!
Here is my suggestion in how it could be implemented.
1. We know we'll get access to collect gases, and also seperate gases from solids. So I suggest that engines utilize this effect, where fuel is getting better as we get better access to minerals and more energy dense gases with different characteristics.
2. Hardpoints already have 4 connectors, so use them! Connecting 1 fuel line to the hardpoint gives you X speed, and one fuel line comes with the standard fuel that exists within current fuel tanks. Connect 2, and its a normal multiplayer minus added heat. For example X*1.9 since 10% is lost in heat. 3 fuel lines would mean X*1.9*1.9. So if X = 10 m/s in a ship, connecting 1 line = 10 m/s. 2 lines = 19m/s. 3 lines = 36.1m/s and finally 4 lines = 68.6m/s. Assuming heat doesn't also escalate with it, with only 10% penalty per step.
This way a ship starting with 1 engine and 1 fuel line and fuel pump (fuel pumps have limits for fuel flow), it'll go slow, but as we advance and gets access to better fuel pumps, or more of them, we can add more fuel lines. The same volume of engine space, gets more and more effective and "speedy". Reducing the need to spam engines as a ship expands so much.
3. As we get access to factories and atmospheric pumps, we star to get access to different gases. Using a pure gas as fuel shoud work in its own, but blending different gases from different fuel-tanks should give different results, and we min/max the mixtures through the hardpoint/or fuel pump.
Using ICE as an example. It can be split into its contents, and some of those gases would be Oxygen (O) and Hydrogen (H2). Set up two fuel lines and connect them to the hardpoint thorugh fuel pumps, and start to adjust how to mix them together. A 4% H2 +96% O mix is needed to get the engine working. But it wouldn't be as explosive as mixing 18% H2 and 82% O for example, where the mix becomes hugely explosive. Risk vs Reward. Making dangerous mixes of fuel makes the engines overheat faster, but it provides max thrust in shorter amount of time for faster acceleration. Unless you let it go and it overheats and explodes. Test out lean and rich mixtures for efficiency and heat management benefits, or add in small amouts of other gases taken from Ajetite for example.
Point being, fuel is how we get the effect that is whished for within the OP of this thread. Discovering the perfect mix after trail and error where some ships have exploded is just fun, and valuable within a company. YOLOL scripts to differ the mix to make it run on its edge of heat tolerance becomes possible too. Efficiency and range and/or explosive for burst and acceleration and maneuverability.
There is no need for "tier 1,2 or 3" engines when one engine can do all of the same steps (outside of shapes), and be more naturally linked to progression through better and more scarce access to different gases with different effects and optimal blending rates vs X other gases. Solid state storage could also be a next step above pressurized and cryogenic storage of energy. Perfect match for factories to produce better and better fuel over time.
4. If max speed is 150m/s then allow all (almost) ships to reach that speed. The only difference between them should be time to get to 150m/s and fuel costs to maintain 150m/s + penalities to play with faster and faster acceleration to reach it. Penalities are heat generation and consumption on equipment overheated, plus higher consumption for that period after.
Two ships with same amount of engines can be different based on how fuel is mixed and played with. One only have 2 types of fuel tanks of O and H2, and the other have 3 with O, H2 and X gas. X gas is used in bursts with the O+H2 mix to reach 150m/s faster than the other, but that burst of acceleration produces a lot of heat which increase consumption for a while after at 150m/s speed. For example.