Hm... just adding in my two catnips here...
The way I see things, it seems to me there should be two types of experience gaining going on here.
The main experience gain from the player/captain/commander to be used for general type of skills, i.e. bartering and trading skills, faster repairs out of battle, faster movement, higher efficency in making munitions from supplies (making more with what you got); general types of skills that can be used regardless of ship types.
The secondary type of experience going into ship types, after all commanding a small little manueverable frigate isn't quite the same as captaining a big giant multi gigatonne hulk of armor and weaponry. Experience gained here only affects the ship type (ie, frigate exp affects all frigate types, all capital exp affects all capitals). The skills related to this are more for combat, i.e faster reloading, better aim, improved crew co-ordination and stuff like that?
Sorry if it doesn't make sense. Y'know, that catnip chew toy is really distracting and all, and the voice ofmice are everywhere, taunting the cats' inability to get cheezburgers.