Well, I'm sure it does significantly more damage in one shot, but it seemed to slow down Samus's movement enough that we were too slow to even react to the Ghost's appearance, so I'm not sure the increased damage is worth the extra high DC.
Charge beam shot is about three times as powerful as a normal shot.
Imagine it like this:
Particularly powerful modern grenade: 1 damage
120mm tank round: 12 damage
Spazer Beam: 15 damage
Power Beam: 20 damage
Federation Assault Rifle: 30 damage
Federation Assault Rifle Charge shot: 60 damage
Charge Beam: 60 damage
Wave beam: 60 damage
Morph Ball Bomb: 60 damage
Missile: 100 damage
Charged Wave Beam: 180 damage
Power Bomb: Fuck you.
Zero Laser: I'll let you use your imagination.
But keep in mind, charge beam involves charging up the shot to do extra damage and it takes a second or two to charge. And while the wave beam doesn't have the same rather insane rate of fire as the Spazer beam it still fires rather quickly.
And for those wondering, yes the Federation Assault rifles have the same fire rate as the Spazer. For those wondering how Samus was supposed to keep up when she was in the federation do keep in mind she's also much, much faster than any marine can hope to be. Also I have no idea why she wouldn't have had missiles and whatever when she was in the federation. I'm just assuming since it was Federation issued gear she returned it when she quit before doing her Zero Mission.