Let's comare the Pulse Phaser with Starfleet's hardest-hitting Phaser, the XIIIS:
Description = "PHASER XIIIS"
Cost = 1950
Mass = 450
Health = 55
Energy = 12.0
Damage = 12.0
Description = "PULSE PHASER"
Cost = 1250
Mass = 275
Health = 30
Energy = 6.0
Damage = 8.0
The effectiveness of a weapon can be summarized through Cost/Damage Efficiency, Mass/Damage Efficiency and Energy/Damage Efficiency. In each of these categories, the smaller the number, the better.
The XIIIS has the following summary:
Cost/Damage Efficiency = 162.5
Mass/Damage Efficiency = 37.5
Energy/Damage Efficiency = 1
The Pulse Phaser has this summary:
Cost/Damage Efficiency = 156.25
Mass/Damage Efficiency = 34.38
Energy/Damage Efficiency = .75
The Pulse Phaser wins in all 3 Efficiency categories, most notably Energy/Damage Efficiency (a whopping 25% superior over it's much larger competition).
The Phaser XIIIS does more damage at 100% power, but a pulse phaser overpowered to 200% does just as much damage (at range 6 or less) AND has the ability to pierce shields, AND is almost half the weight.
The XIIIS has only a couple of advantages: longer range, and superior damage when overloaded. And look at all the disadvantages it has to take on to get those 2 advantages over the Pulse Phaser: heavier, costlier, no shield piercing, far less efficient, requires more energy.
You can conclude from all this that the Pulse Phaser is a very underappreciated weapon. 200% Power to this weapon gives you 12 points of damage to deal to your opponent (per shot, 1.2 points of that damage getting straight through the shields, on average). For the damage it does, it is incredibly light and efficient. The much-lauded Quantum Torpedo does only 13 damage at 100%, and is less energy efficient!
I think the reason behind the Pulse Phaser's bad press is due to the very wimpy sound effects it gets in the game, creating a psychological effect leading the player to believe they are far weaker than they really are. But if you look at the numbers, that just isn't the case!
So don't be afraid to use the Pulse Phasers, they are worth every PP you spend on them. Just remember to give them plenty of overload power, and you have one of the best weapons in the game!