The reason i suggest something like this is to stop what ive seen as capital ship spam. Not necessarily on part of players, but on part of the AI. they spam flagships at you like the pirates spam raiders.
My idea was to have people invest more in capital ships that they already have built, rather than to just build more. Capital ships are strong, there is a huge gap between a fully upgraded starbase/titan and capital ships.
Maybe it could be setup so once the ship had acquired the required experience to attain level "11" you would have to buy the level. Say 5000/500/500 to get the next ability. Like you would do with a starbase, but you would buy the upgrades for your capital ships. I can tell you if i had 50,000 credits invested in a couple ships i would make for damn sure they were protected.