You seem to play with people who are into making "the winning combination" rather than ships with some sort of concept.  In roleplaying games, this same thing is called "min/maxing" 
Try designing a ship that fills a certain niche in the fleet, rather than just trying to find the best bang for your buck.  By this I mean, small fast ships with light weapons to handle escort or antifighter duty, long range battleships for bombardement, quick ships to function as wolfpacks to handle straglers on the field, etc.  Try to design ships as a real world military would. 
Our military engineers COULD design a working high altitude stealth bomber with 18 150mm cannons on it, but why would they?

Amen ta that.

Hello everyone from Jacksonville,
My friends and I played two games of Starmada today using the Two Weapon-Trait limit, (Acr & Prc don't count against this limit).  The games were fine and lasted a little longer, and were less brutal than before. 
Some of the weapon combos we had on our ships included {Dx2+Dx3, Slow+Cts, Dx3+Cts, Tls+Dx3, Dfs+Rpt}.  All of these weapons also had Acr, and none had Prc because no one here used shields.  In fact, all of our ships have Fragile Systems.  One of my friends has Long Range Sensors on all of his ships, I have Overthrusters on all of mine, and another friend uses neither.   
I think we have made things unbroken, and made the game more fun to play. 8-)

I do believe that it was an Oops that has allowed the use of more traits than in Admiralty.
I have always resisted the temptation of putting silly* weapons on ships with one exception being an alien planet killer.
My thought is that there is no point in playing any game where everything goes Boom in the first turn.

How many weapon traits are allowed by the drydock?
I have thought of restricting the number allowed in shipyard nova a few times but I would not ban the use of expendable as it does have its' use (not to reduce cost) in conversions.

* Weapons that use traits to multiply the damage to the point of a fairly sure kill on the first attack.
This is just my 2d(Old Money)but it seems to me that it is an upward spiral, weapon does more damage > bigger ship > weapon does more damage > even bigger ship . . . .
Might just as well throw one D6 each, first to get a 6 wins!

Paul

How about the following:

The game will probably be a more enjoyable gaming experience if you limit weapon traits to two per weapon.
Thank you, and have a nice day.

Kevin

You could try adding a note to the design section of the book. Something along the lines of talking about the eggshells with sledgehammers potentially reducing the fun of the game, and that only designing ships that are powerful and not fun kinda misses the point of the entire designing system.

My friends and I are playing Starmada, here in Jacksonville, at Suncoast Comics near NAS Jax on Roosevelt Blvd. 
All are welcome. 8-)   
We will continue our restriction allowing only two weapons traits on weapons, with Acr & Prc not counting in that number.  Also, although we don't use Expendables, Seekers are allowed...