In my, won't admit how long, time as DM'ng I have picked up a few things. Related:
One is that LordBlades is correct that mid-powered groups are the easiest to DM. A 1st-3rd level character in D&D for instance can die with a sneeze, and you have to be very careful in choosing challenges that won't accidentally TPK. At Mid range, there is plenty of things that will challenge/frighten the players, and plenty of things the players will frighten. The second part is just as important as the first: The players should be allowed to FEEL the power they are accruing(or starting with). . . and if you have a combat leaning party, that feeling of power should manifest in having combats that the players rip through with ease(not every combat mind you). And if my players min-max a shooting ship in RT, they will get the opportunity to own opposing ships with it. We all enjoy the feeling of success, and mastering the rules of the system is a means of EARNING that success.
Second: As GM, it isn't my game. I am the host and referee of a social event, not a god deigning to spend time with lesser beings. My goal is for everyone to have a good time, and "Rule 0" is something that can undermine that fun. The rules are the foundation of the evening, one which the story and events are built on. Both the players and the GM will abide by them. If it is apparent that the rules are up to DM whim then that foundation becomes fluid and undependable. The player's ability to act with confidence is undermined. (which already happens to some degree since this world is so far different from their own. Modern settings are easier that way)
By limiting myself to the rules (and being a bit flexible when adjudicating on behalf of the players), the players feel empowered, have more fun, and keep coming back. Set the scene, and hands off. If the players kill the big bad in one hit, so be it. (though I may delay the moment of death in order to get all the players an attack; minor fudge they tend to not notice and enjoy more) Many times I have witnessed GMs who didn't realize the only reason the players were having fun was because they were hanging out with friends, and that they were hindering more than helping. Gauging how well the GM is doing can be quite difficult with social games, as friends hanging out will tend to have fun regardless.
To bring it back to ship creation: In the 2 games I recently started running(one already going, the other soon to start), Players go through the Warrant & Origin Path for storyline background. .. but PF is fixed at 20, SP at 70, and whatever isn't spent on the ship goes to PF. This allows them the most freedom (both story and gear wise), without the randomness of the Core's system, or the min/maxy of the ItS setup. Max out SP and start with low PF? Peachy, the players get some fun space combats, but hope they didn't choose to be armed with torpedoes. Opposite? Peachy, they will run from space combat for awhile, but . . . etc. etc. etc. . .
Teleportarium is a complication though. I'll probably leave it with the once per major encounter thing. If the players choose to have something they only use once in a while that is on them. . .
Whenever I've theorycrafted a ship for play (I'm always the GM in RT, so sad ), I've typically gone for the small cheap ship and kitted her out to the nines, figured survival in space trumped all other concerns. Recently however I have been attracted more to the idea of a half-mothballed cruiser+ sized ship which is barely equipped. . . like an Overlord with 2 guns and a couple supplemental components. Not effective in pretty much any way, but would go well with the theme of rebuilding a near ruined House. Call her the House of Usher or some such