Possibly the best (and most enjoyable,) experience in this mod literally happened as I am posting this.
Ok, so I got The Osprey and named it the "HMS Gonna Live 2" (I already had the HMS Gonna Live as my second best score). Ok, so I will skip through this for everyones enjoyment. I had on the ship (as far as I can remember)...
-Full shields (Only need three for the boss, but decided to get 4,

)
-Full engines (48% dodge chance)
-Full artillery beam (Fires every 20 seconds)
-1 Burst laser II
-1 Ion bomb
-1 hull beam
-1 pike beam
-Maxed out number of crew containing all races except Crystal.
-
three automated reloaders
As I went through, I was literally DESTROYING all the ships in my path in 30-40 seconds. As soon as I got to the boss, I first got rid of half of its shields with Ion bomb and shot a full weapon arsenal on top of it all.
First and second stages, boom, done.
Ok, so my ship was at half health at the beginning of the Third stage, but fully repaired systems. As I jump in, I
notice that the Flagship is next to a star. Ok then... then I notice...
I had no cloak.
As all of you may know, cloaking is mostly
essential if you want to beat the final boss. You don't really need it (if you want to have a hardcore challenge) but that is what blew me up.
FINAL SCORE: 3654
I lost because I had no cloak 
However, dying is part of the fun in this game, so I'm not really worried.
It's just the matter that I had possibly the BEST run in the game so far, and suddenly it was all halted by the Third Stage of the Flagship.
Usually with this mod, I don't even make it to the final sector, let alone the boss.
FINAL THOUGHTS: This mod is possibly the greatest mod overhaul for FTL I have ever played. It adds a "harsher, but richer" playthrough across the galaxy. I would be happy if this mod continued to add stuff, and I would still play it if it went dead.
I'm never going back to vanilla... that is, until the Advanced Edition...
But for now, this is the best mod for FTL so far. 10/10.