I like the ship creation idea, if the opponent ships are created with the same system, could you salvage their components and attach them to your ship after a battle, and also use their tech to increase your tech level? I think having lots of tech levels would be good or maybe 6 major ones with sub categories, so if you got tech that was too far ahead of your own then you wouldn't understand or be able to use it until later in the game. I know you said it's not a combat game, and it should be really hard to take down another ship. I was disappointed at the amount of stuff you could recover from another ship in FTL.
Well, my idea is that if you can salvage components from outside your tech level, you'd probably want to build a ship around them. But ideas on that front are still pretty foggy, haven't gotten that far - but, for sure, integrating another ship's parts would be a major undertaking on par with building a new ship.