One aspect of the present version of the game that drives me nuts is the warped reality that results in the ability to build a spaceship faster than it takes for one to be destroyed. Obviously, this isn't always the case, based on what sort of carnage is going on but it still ruins whatever tiny bit of immersion that exists that these are real empires going at each other rather than spawning Space Invaders that just keep regenerating as long as the cash holds out.
It makes the game a wearying experience to keep piling guys into a battle hot off the assembly line while the enemy does the same.
I wouldn't suggest making the destruction time faster but rather making the build time a lot slower or at least making that a gameplay option. (It would certainly put a lot more value into putting multiple frigate factories in a system since as it is right now I can just crank out vessels from all corners of the galaxy and rendezvous at whatever the current hot spot is.)