I wondered if it would be worth considering an option to allow your ship's warp core to be modified. This could be done through crafting, the application of skills you or your bridge officers acquire, quest rewards or a combination of these things.
An upgraded warp core might allow you to go faster, to have a better turn radius at warp or it might provide a bonus to your energy. These buffs could be time-limited or create instability in your ship systems. Perhaps akin to engineering in WoW, where a trinket could fail, sometimes spectacularly. As the captain, you would have to decide if the benefits outweigh the potential risks.