When in doubt, stay close to the existing system.
It's so easy with these kinds of things to go overboard in making something totally customized, but for playability and integration, it's always best if it doesn't stray to far. In this particular case, that means trying to stick with hull, strain, armor, maneuver, action etc as written unless we really need to change something.
Keep the focus on the Heroes/villains
There are hundreds of people on each ship, but the ones we care about are our characters, and the notable antagonists - for capital ships, that means our senior officers. So the decisions, effects and rolls should be based on our senior officers when possible.
Keep the game moving
The trick here is not to get caught up in such a way it takes forever to complete a battle scene. The big thing here is minimizing rolls. In addition to keeping the number of rolls down, however, is reducing wait time, particularly for a PbP. This means trying to make multiple rolls occur at once, and otherwise try and minimize back and forth. It also means minimizing roll-effecting-rolls when possible.
Ship and crew matter
This is basically the balance point we're going for. A ship with a PC or Nemesis captain or crew should be able to punch above their weight, but no so much that the quality or strength of the ship doesn't matter. PCs should win against 'rival' ships of the same class, but not without some damage, and Nemesis ships should be close to equal. Likewise, PCs should be seriously challenged by 'rival' ships of a slightly larger class, but able to win with high skills or good tactics. We want to avoid creating a situation where the presence of the PCs or the size of the ship are the only things that matter.