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.
A lot of people have suggested this, myself included. I think each tier of ship should be able up get a new warp core installed.
The basic warp core type we get with starter ships should be what we have now. For each tier up, we should be able to craft a new core from memory alpha that gives a slight bonus to power output depending on the ship type with a secondary bonus too and a slight bonus to power transfer rate.
So for each tier up, the bonuses could be:
Cruiser: +1 to all power levels
Escort: +2 to weapon and engine power
Science ship: +2 to Aux and shield power
All: +20% power transfer rate