Weapons pre-igniter is awesome and made me awesomely powerful on that one time I managed to get it. :). especially because you don't waste scrap on repairs thanks to it (take out their weapons first).
Anyway, my tiny lasers themselves were not doing much to that well-shielded ship. I don't think the OP's point is very valid near the end of the game.
I explicitly said that the Burst Laser II is an exception while burst laser 3 is unviable.
Burst 1 is 2 energy for 2 shots at 11 second charge. Burst 2 is 2 energy for 3 shots at 12 second charge. That is the most significant upgrade in the game I have seen yet as it actually increases your DPS rather then decreasing it. As well as being able to penetrate 3 shields (1.35 on average against max dodge enemy though)
Of coursing mixing the two is a disaster because they will go out of sync due to that 1 second difference unless you fire them manually (which will lose you precious seconds)
4x1 weapons will rock until late game but you should upgrade some of them to 2 energy weapons.
The problem is that almost every "upgrade" reduces DPS per energy significantly. A typical upgrade is 50% longer charge time 50% more damage for 100% more energy or 100% more damage for 200% more energy. This is a massive downgrade in terms of DPS.
The only reason to upgrade is because you have only 4 slots. But the fact you max out at 8 energy for weapons means that 4 energy weapons are unusable and 3 energy weapons are highly unoptimal (can be used in conjuction with 1 energy weapons but its better to have 2x2 then 1x3 + 1x1)
Best playthrough I had was 3xBurst Laser II and 1xIon 1
Shredded the final boss like wet tissue paper.
2xBurst laser 2 + 1xion 2 (3 energy) + some 1 energy weapon would also probably be very good.
Problem is in FINDING the weapons you need.
Drones and missiles can be effective but run out too easily. So you must be able to beat normal enemies with them to save them for the big fights.
And drones cost an arm and a leg to add to your ship.
I'm not sure having just got the game Friday, but I've noticed in later sectors shots get resisted on hits occasionally. I wonder if this only affects the lower their weapons.
One of the augments allows a 15% chance of resisting weapon's damage.
Now one should also consider that you have only 4 weapon slots, so, 4x1 is still waeker than 4x3 weapon power.
How are you powering 4x3 weapons with a total of 8 energy max? you are going to be powering 2x3
Which incidentally is even worse then 4x1.... but 2x3 + 1x2 =8 so that is the ideal configuration for a ship with only 3 slots. And a non ideal but still workable config for others...
Now the Burst Laser 3, that stuff is trash. It fires 4 shots at once, like 2 burst laser 1s would. But it has much higher recharge rate for worse DPS coupled with requiring 4 energy to their 2 (1 energy per weapon)
If I had to sum up my issues:
1. "upgrades" to weapons significantly reduce their efficiency. (DPS per energy)
2. Shields are unbalanced.
3. "upgrades" generally take up too much energy to be used viably.
4. A weapon cannot be partially powered so 3/4 energy means your 4 energy weapon is completely down.
5. mixing varied weapons suffers from inability to group weapons to fire in tandem. (which requires a lot of pain manually firing them in tandem).