Upgrades should always improve the ship! (Burst is a bit broken)

Burst is not broken. It gives you twice the damage with some penalties.
The penalty is more convenient on some weapons but for some it is not working well. That much is true.

Part of your job as a captain is to find out what kind of weapon mix is working best for your fleet.
Sometines burst is a waste, sometines it works just right. Part of this depends on luck. Some weapons you can find seriously alter the best setup (like Heavenly Dual Ion Cannon)
That is making the game intersting and challenging. But I agree that sometimes more transparency may be nice.

In general bigger should however not always better!
Making thinks always bigger is simple. But in the end you would have installed super weapons only, no thinking required.
(And in real world terms indefinite power supply, storage area for missiles or tareting computer power are just not real - or painfully expensive...)

The choice of the best loadout is a key to the game. So it should be challenging and something to think about.