I think the idea of a "super ship" has some merit, but would take a LOT of careful planning so the first person to build this ship doesn't just steamroller everyone else. You can do that already if you build the max number of capitol ships (16), pay for the first few upgrades, add a few carrier and support cruisers and put them all in one fleet.
As for busting starbases, all you need to do is build a secondary fleet that consists of 6-10 of the new sturcture busting cruiser (the have a larger engagement range than even a fully upgraded starbase) and have your primary fleet (set to hold position) guard the secondary fleet. Even a fully upgraded starbase won't last more than a couple of minutes at best.
I think a "super ship" should not be heavy on weapons or armor, but have on or two "super special" abilities, like the ability to destroy all tactical structures, or ships, in a system at once. But before anyone freaks out at this, the ability should take a long time to charge (about 2/3 the time it takes to build a starbase, or so), and the ship must be at the target planet before the ability can charge. This could be useful in attacking pirates.
That being said, I think one would have to be very creative to actually make a super ship work in-game, because of how big you can make a fleet now. (see first paragraph). However, new ideas are an awesome thing. Not eveyone that has ideas can build mods, and people that build mods can't have all the good ideas. Keep the ideas flowing, xploseve_12b.