So I had an idea the other day... that I know has absolutely no chance of ever actually happening, but I thought I'd share regardless.
When we design ships, instead of endlessly applying components, we have three wheels just like the governance wheel.
Wheel one, is splits your capacity between "components", Weapons, and Defenses. Wheel two then allows you to split your defenses into the appropriate three categories as you like, and wheel three the same for weapons.
You can then use checkboxes to apply the non-weapon/defense components that eat up the component capacity you gave the ship.
The idea appealed to me, because it quickly allows you to make that new "missile offense, beam defense" ship, and it would remove 'components' as a physical piece of your ships (which I always hide anyways). It would likely break down, in regards to technologies and how they would apply to ships... you'd likely have to make all upgrades generic and apply instantly which would be lame.
Don't get me wrong, I like the current system well enough.