JPS-205 I'm afraid that a ship with decent point defense or the new flak will easily defeat yours. Right now you rely too much on ending the fight in one blow, which probably works fine against most built-in ships of vanilla Cosmoteer.
This mod however is filled with some of the community's most deadly ships, so if you want to add yours to it I suggest you sharpen your skills by reading this guide: https://forum.cosmoteer.net/d/7783-cosmoteer-ultimate-ship-design-and-part-guide .
If you already have done this, I would do it again since your ship still shows some of the dont's mentioned in this guide.
The problems with your ship you should be able to fix (Note: these are the things I see without opening your ship in game. So I have no idea if you spammed doors or made some other mistakes at the interior of your ship) :
You have no reverse thrust and all thrust is located on the back of the ship. Your ship can move, but will have problems when facing more mobile ships. Move some engines to the front having more reverse and sidewards thrust.
The shields are quite unprotected. Once out of power they can be attacked and taken out.
FTL-drives add extra cost without adding any use to the ship. (Your ship will be an enemy, not a ship the player will use.)
Clustered reactors. One well aimed shot of a railgun and your entire ship is doomed. (Of course, any weapon can do this, but railguns are the best at abusing this weakness.) You don't even need three reactors. One should be doable, two would be ideal. Just make sure to have them separated and next to a shield.
The nuke factory stands next to the reactors. I think you understand why I find that a not so tactful choice.
Too little firepower. I know the nuke packs a punch, but it fires slowly. This means misses will be punished a lot. Your mine launchers will also have little use since you have no reverse thrust. This way your ship will ALWAYS be chasing another ship, lowering the chance of hitting a mine.
Hope this helps, keep trying and never give up! You'll make it eventually. π