I'm going to complain a bit about dead crew regeneration. While I appreciate the resurrection of dead crewmembers for convenience sake, there are realistically only so many replacements to be had on board. While it is technically feasible to rebuild a crew without going to spacedock, this process would literally take decades. I suggest that a permanently dying crew would add great depth to the game, upping the (currently very easy) difficulty and making the management of ship resources much more important (thus steering combat away from being a bit of a button-masher, as I've seen some call it.) Loss of crew already impairs one's ability to fire weapons and repair the ship, which is an ideal thematic element, but the superfast breeding nearly nullifies this element which, as I said, should be a great strategic part of the game.
On teams one might be able to do "crew sharing" amongst fellow team members, to prop up a damaged member of the team without having to wait for a long trip back to Spacedock and back.
On different note but same subject, it would also be ideal to have a limit to the extent that one might be able to repair his ship in the middle of space. On a severely damaged starship a full restoration would take weeks, perhaps (and has, in the shows). Capping in-field repairs at 50-75% would provide a good realism, I believe. Or one could have an "onboard raw materials" reserve that, once depleted through repairs, could only be recharged at a starbase (or with collected resources).