Just a thought that i had when i read your post on SuperShips,
It reminds me a bit of when i played GuildWars, and had a Monk, and a Warrior, and later an Archer, was that i spent ... like hours... and hours leveling and honing and getting certain charms that you could find in only certain parts of the game world. So what it amounted to was a custom Character. No two Monks were completely the same, some had aggressive powers, some passive, some were african and wore sari's and beaded necklaces, some were pristine blondes with greek white robes and sandals and picked up powers from deep in the game where some made it, and alot didn't.
The point here that i'm leading to is this. What if we had a mod, haha, yes, a mod, because surely we can't turn the game "completely" upside down.
We make three or possibly four capitals, these are SuperCapitals, they level, but way ... way beyond 10 levels. And the ability slots are variable, i can make it a SuperMarza, or a Havoc wrecking Advent Carrier... or the Vasari Dreadnaught. But here is the difference, YOU pick the abilities. Out of how many? three dozen abilities? Four or Five dozen? So each ship becomes a unique craft, a unique character. And the ships should have more than 4 slots, or now 5 in Entrenchment. Have a page... like the research tree pages where each ability is activated, but they cost a horrendous amount. And it takes time, im talking huge amounts of time, maybe hours to get to one level, half a day to get to the next, three days later to get the next one, and a week for the next...
This all implies of course ships that carry from game to game, or else at least one long.... super long game where i could colonize and ravage or get my self kicked and killed in a few weeks time. This means expandable maps, maps that can be added to without starting over from scratch with the ships we have. Ok its a sandbox, but why not make it a HUGE sandbox? WIth thousands ... of worlds. 
Give me one ship, and have me lay waste, and almost get wasted myself in the beginning fighting off small bands of Pirates and Militia, but later, i dont have to even blink to turn them all into vapor. So where is the challenge? Why its in that SuperMarza that has skittered across my holo-screens several times on several worlds without us yet engaging. That is now almost level 19 and im still pushing 12. And he's got the guns, but i've got shields and armor that say bleh and we slug it out for hours, turns and fights, the planet gets in the way and get torn up, not because we're fighting for it, but because its between me and my enemy and we keep scarring each other up. Prowl and turn, fire and bank. Until one or the other retreats, not because we're half dead, but because we need to go level somewhere to get another set of abilities to add.
I dont really know if anyone but me thinks this is interesting or not, but it might be like "Submarine warfare with us having a lone ship and slipping under the waves or on top for attack and retreat, plotting courses and readying weapons to take out the enemy. 
Haha, boy silly thought tonight, but it might even be a lot of fun. Superships that keep leveling and leveling against all the other AI. Or multi-player where you bring your custom made Capital and Lay waste and get wasted, but never really have to start over. Just walk away with your Horrendous Havoc Carrier and get some more levels and come back. 
... I seem to have this obsession with the starting over thingy, haha, i haven't figured out exactly why yet, but there it is. I just "wanna" keep building and going on... and on...
Persistent i think is the word. Yes, persistent.

Good idea though in your post, SuperCapitals, i like it. 
-Teal