...Now I'm trying to figure out what it'd take to make that work well.
Option 1 (the night killer):
Design a fast battlecruiser - really fast, Odyssey fast - with mostly forward hardpoint weaponry (say, two large energies and a large synergy, plus some medium energies, medium missiles, and a few small universals). Give it something really abusive for a ship system - a better mine teleporter, or multi-EMP arcing, something to really sell it as evil and powerful. Armor it like a proper battleship. Tune it so that it murders everything smaller, but relies heavily on phasing and its ship system to win against other capitals.
Option 2 (the mothership):
Design a heavily-armed cargo capital - something like the Atlas Mk2 with narrower arcs and slightly less direct firepower - with an emphasis on missiles (call it three medium missiles, a large synergy, a large energy, and a sprinkling of small universals and energies). Give it a ship system that synergizes with a fleet of other ships; a brakefield, a super-jammer, whatever. Armor it like a battlecruiser; enough to take some hits but not so much that you can wade in shooting without a plan and backup. Tune it so that it's mainly there for amplifying the effects of the fleet it leads and throwing the final knockout punches.
(Part of the inherent problem is that phase ships are designed as 'one class above' in power, so a straightforward capital phase ship relying on capital levels of firepower would be a supercapital, and those... just aren't fun to pilot. Most of the way line combat capitals behave - racking up huge flux debts in the course of a battle and lumbering around ponderously - doesn't mesh with the way phasing plays).
The lore explanation for why something like this exists would be interesting. What's the utility of a phasing capital ship in-universe?
