Ebolav wrote:*snip layout*
Sounds like a decent ship. The big problem is lack of mind control to offset their mind control. If you have extra scrap still, upgrade all of your systems for the buffer zones, to keep the enemy boarders and mind-controlled guys from wrecking them.
Few questions re: lv 3 rebel ship/in general
-For most late-game ship I can't see the benefit of boarding. Basically I teleport in, wreck the first two crew down to critical, but before I can wreck the ship 2 new guys sub in, and I have to teleport out. Is it only worth it to teleport in against weak races (slugs, engi), or ships with less than 3 crew?
Boarding is harder in AE due to clone bays but not a lot harder. If you have elite fighters you should be able to destroy the clone bay with your weapons and then kill the crew with your guys. It takes practice and persistence, though.

Ebolav wrote:-Against lv 3 rebel ship, is it worth it to try and disable their drones instead of weapons systems, so I can then switch to my breach missiles without them being shot down? Seems like late game, missiles are too hard to hit with unless you focus so much effort on taking out the drone systems, effort which would be better on just hitting the weapons?
I assume you mean the 2nd stage of the boss? The 3rd stage has no drones.
Taking out the drones in the 2nd stage is second only to missiles and sometimes not even that. If you've got a breach missile I'd pummel his drones to take them out and then breach the missile room. Don't be quite so concerned with dodging, the flagship's dodge chance is not the same as most of the ships you've been facing in the last sectors. He'll still dodge, for sure, but not nearly as much as those auto-scouts you've been tousling with to get to the flagship.