I was thinking, maybe for 1.3, the developers can add a button that resets a civ's abilities, and one that clears all custom ships for all races. For example, you're playing as the humans, and you change your abilities, since the abilities are set up by default in a way that's immpossible to duplicate by using custom abilities, you can never reset them. If there is a button that does this, sorry, but I've never seen one.
If you think this is a good idea, please implement it in the next patch. By the way, this is a great game, and this is pretty much my only pet peeve with it.