I've decided to do a bit of modding myself and have decided to make a playable rebel flagship.
Most of it is done whats left is the gibs and weapon mounts
Not possible to change weapons to artillery

Replaces slug A and b
Download below.
Let me know your thoughts on it.
Bren tenkage did a lp of the mod in the post below
Dropbox link: https://dl.dropbox.com/u/49965727/Rebel%20flagship.ftl
varient b https://dl.dropbox.com/u/49965727/Fed%20flagship.ftl