Hello, everyone!
I previously had a post about this mod, but this is a more complete version of the matter, so I'll just start over.

Based on the "Flagship Randomizer" (located here: viewtopic.php?f=11&t=26241&start=180), I offer the following mod for the FTL Community: the Custom Flagship Set. Rather than having purely randomly generated Flagships, what this set contains is 26 human-made Flagship designs that are thoroughly tested and intended to be balanced, but with a wide array of different styles and challenges. That doesn't mean everything is perfectly done, but it DOES mean that you can have an interesting fight each time and know for sure that the battle will be worthwhile - and also different, every time.
Included is a tiny program that will pick a random Flagship for you and shroud its name so you don't know which one you're fighting until you get there. You can choose to keep playing against the same Flagship each time, or randomize it every game if you like. Just make sure that the list of Flagships is in the same folder as the randomizing program, and you're good to go!
All you have to do: make sure that the mod "Custom Flagships" is the second-to-last mod in Slipstream, and make your Flagship choice the very last mod in Slipstream - engage the mod, and you're ready to play!
Additionally, I've added a customized version of FTL Captain's Edition that makes all the ships in the game have different starting layouts, just for a different feel if you like (every ship costs between 996 to 999 scrap when all systems, ammo, and crew are added together...call me picky).
Enjoy, everyone! And please do send feedback - VerdenLeafglow@gmail.com
So just as a recap, to run the mod...
-"Custom Flagships" should be the second-to-last mod in Slipstream
-The Flagship Type (A to Z) should be the last mod in Slipstream
-The CE Mod ZHO is NOT necessary for this mod at all - it's just my personal take on Captain's Edition and you can use frankly any mod you want with the 26 Flagships and in theory they should all be compatible
Cheers!
-Gidoza
https://mega.nz/#!YgVEVQwY!N8Gno9g2Wz__ ... hqI8v-r2Bw
EDIT Dec. 21, 2017: Just a note that the mod SHOULD work with basically any other mod as well as Vanilla. The Flagship mod itself only affects the Flagship and is totally independent of anything else, so you won't get any conflicts, but it's for AE only.

EDIT Dec. 30, 2017: New version out, version 1.1 - Fixed a bug whereby Drones on the 3rd round against the Flagship wouldn't launch (for the Flagship). It should work fine now!