I find it a little overpowered when, during fight, you can instantly repair your ship (should you have the cash spare, which I often do) I think a better idea would be to have crew repair your craft once you pay to repair it, and so it begins to "regenerate". that way, crew needs to be spared for repairs, and also it means that you have to be certain you are safe before commencing any repairs. sounds fun eh?
also, I would like the addition of docking ports, allowing you to board enemy ships and "take over them" (as apposed to blowing them out of existence) or to transfer crew to one of your ships which is in need or support (such as carrying out repairs, e.t.c)
I think these two additions would add a healthy amount of difficulty and planning to latter stage games, requiring a better balance between huge hunks of armor, and lots of functional parts.