I was going to PM you my blueprints for the boss, but I thought other people might want to take a look, so anyone who's interested, follow this link to see how I've personally been playing the final boss... Except for this I lowered the Boss's health so you can get through the stages quicker and see each one.
It's a .ftl so you can load it after Captain's Edition just like anything else using Slipstream. I only changed the blueprints of the Boss so it'll work fine. Also, copy and paste my continue.sav file to its proper place to jump directly into the final battle with the overpowered Red-Tail I used for testing!!!
Boss Blueprints.ftl:https://www.dropbox.com/s/pmgc0d3424ctp ... prints.ftl
Here's a taste... Apparently having an AP drone and Repair drone on the first phase isn't as much of a pain as I remembered. I was able to take both the lasers and missile room before the first artillery even targeted me. keep in mind though I did disable the Boss's cloak, I have max teleporter and cloaking (I abused the heck out of cloaking), and 4 people trained to the max in combat.
EDIT: Links to images if they're not working...https://www.dropbox.com/s/u6r0lr380rbwg5h/img3.pnghttps://www.dropbox.com/s/rtmoyw2ryejvrze/img4.png
I suppose a "normal" boarding ship with 4 people could theoretically do the same thing. All you need to do is teleport into one room, and keep the AP drone distracted long enough to take out the other room as you can kind of tell from the pictures. However, it is extremely risky without disabling the Boss's cloaking unless you are constantly keeping track of the time between cloaks.
PRO TIP: Since doors have been added it is possible to change the positions of your crew while fighting. If you don't know how to do this now's the time to learn because its kind of crucial here. You can pause, select both crew, send them to another room on the enemy ship, then select them again and "send" them back to the room they're already in, but in the order you want starting with the top left corner.
Some other minor things you may notice if you download and play this. I switched the sensors and doors room, why? So the Boss can have doors on the 2nd phase. I added a weapons room and moved door control to the center of the ship. Why? So the boss can use drones on the 3rd stage and I thought the flagship should have a weapons room that looks cool there. I changed the drones on the 2nd stage. Why? because Combat laser and beam drones appear from the power surge I wanted the main drones to be CE ones only, because they look cooler. I gave the flagship 2 extra crew. Why? Because YOLO. :p
And lastly, the events after defeating the boss on the 1st and 2nd stages I was talking about... I really hope you like them.
Anyway, there you go it's late here so I'm probably going to go get some sleep. let me know what you think. Thanks a lot Sleeper and everybody.