To the reactors:
I personally would split them in 2 types of power sources.
Low Power Generators:
(Creating the power of life support, internal systems, etc.)
Solar panel (only work in star systems, could be retracted and extended. Possible are small and large solar cells. Possible aswell large unfoldable solar wings, who can even charge the batteries of the ship)
Fuel cells (need more fuel, but use very common materials)
Radioisotope thermoelectric generators (needs less fuel, but not so common materials)
Small Zero Point Generator (small generator, who creates a low constant output of energy. Needs very advanced technology)
High Power Reactors:
(Provides power for more energy entensive systems like Ion Engines, Plasma Ion Engines, Warp Engines, etc.)
fission reactors (Uran and Thorium reactors, very heavy, only provides a low power output. Thorium reactor is the more modern one who is safer. Very cheap to build, needs only very low tech.)
fusion reactors (stand space reactor, needs a average technology and provides a good power output.)
antimatter reactors (high power reactor, who creates the largest power output. But they are very risky. They need a continues and elaborate maintance, otherwise it can end in the complete destruction of the ship.)
high power zero point generator (needs very high advanced technology, provides a power output similar to a fusion reactor, but over infinite times without fuel needs)
Engines:
Yes, most engines are already there, like
Atmospheric Engines:
Jet (low speed atmospheric flight)
Scram-Jet (high speed atmospheric flight)
[could be combined to one engine, already there]
atmospheric ion engine (will ionize the atmosphere and accelerate it trough electromagnetic fields. Possible for med sized ships (see below))
Space Engines:
rocket propellant (low power, but high fuel consumation)
Ion engines/Vasimir/Plasma engines (needs inert gas, or plasma from a fusion reactor).
antimatter engine (Donno if something like this is planed. Yes, Antimatter is planned, but donno if only for power generation or aswell engines. So an engine, who use the direct reaction from a Antimatter reactor for such an engine. Could possible go with 100g or something, if the ship as some dampers.)
And the quantum vakuum thrusters (http://en.wikipedia.org/wiki/Quantum_vacuum_plasma_thruster This engine should need a lot of power, no fuel but should be slow. So about 1g with a good zero point generator)
For dampers, i would suggest:
pressurized suit (10g)
gel tanks (20-30g, but no control over the ship, so it has to fly with autopilot)
higgs generator (needs very much energy, but would aswell support the 100g antimatter engines)
FTL engines:
Alcubierre (will need a very high power at the beginning. Only the antimatter reactors are able to provide immediately. antimatter reactors would aswell give the hightest speed. Other reactors would need some high power condensators, who have to be charged before they can power up a alcubierre drive.)
Wormhole (The idea i had in mind would be to use some massive gravity mass to get this engine running. Possible a sun for interstellar travel, or a black hole (=D) for intergalatic travel. This has to be tweaked, because it could be a problem, when a ship strands in deep space. Possible would be, that very high advanced ships could aswell travel between galaxies with alcubierre drives and that the player can call for help, if he strands. So it would be more a way for faster traveling)
For the ships, yes the small ships are looking nice. Only rocket or jet/scramjet engines, no reactors (because they are to small)
Then i would include some medium sized ship. They can carry reactors, but are to small to create a own space warp. They could possible use some stationary accelerator, or some space warp ring in space, who is orbiting a star. The ships could hold the space warp then on their own, but would only fly very slowly. So they would be ideal for automated transports between close systems. Other medium sized ships could be used as landing ships for very large motherships to launch larger cargo to the motherships. The larger motherships should be able to transport such ships and it should be good to have one near a cluster of colonies, to pick up some frighters, who had some engine failures between the stars.
The motherships should be of course the only ones to create a own space warp and the only ones to fly with very high speeds.
Feedback:
(I completly forgot it and had to edit it in.
)
The idea would be to give some additional pathes of technology, who are all balanced to each other. So all systems should have advances and disadvances and should have some stages of development. As examples for the reactors, the antimatter reactor would be extremly powerful, but very risky, would need few fuel, but the fuel would be very difficult to create.
The nuclear reactors are solid reactors with a good power output and reliable, but would need a lot of fuel, who is easy to make
The zero point generator should be a bit less powerful, but should give infinite power, but would be expansive and would need a very good technology.
Hope, that at least somebody likes the ideas.