Until this mod gets a serious balance and sound pass, I won't touch it
Specifics would be useful here.
Balance side: One of the biggest things that I see mentioned is your missile cruiser. IIRC, it has 2 large missiles, one medium missile AND Fast Missile Racks, which can easily become stupid OP, even in .8. I would say at least remove FMR AND cut down the mounts to 1 large and 2 mids. That way it is still a missile cruiser but it isn't bulls*** OP.
Also, I would seriously talk with the other modders to see what issues they have with your mod, as sometimes there can be issues that can be right in front of us and we can't see them. Your mod has some nice things but needs many tweaks here and there to get it perfect and the others can help with that.
Working on the rare metals bug will also be good, which was another big issue I had with this.
If you haven't already, please stop replacing the Apogee sprite (and any other vanilla sprite if you do).
Sound side: PLEASE, for the love of the Goddess and everything that is holy, STOP using sounds from famous games (Mass Effect, MechWarrior, FreeSpace are a few that I remember)! It is lazy, can throw off the player and from what I have heard, you can make some pretty damn good sounds on your own.