Given a certain power input level, a pulse laser and a beam laser will impart the same amount of energy on a target in a given amount of time. So there should be no difference between them, right? Well, I can think of a few differences.
Pulse: stores up the charge, and hits you with it all at once. The laser must be powerful enough to handle a large pulse, and must have large charge/discharge banks.
Beam: hits you with it over the course of time. Can be smaller, since the amount of energy at any gien moment isn't as much, and requires no fancy gear.
This is like the difference between getting shot or having some one drop bullets on you over the course of a couple minutes. This doesn't mean a beam laser is worthless, just that its emply should not be haphazard.
Heat is a tremendous killer. You warm some one up faster than they can cool down, and eventually they will get too hot. Large spacecraft with large guns (and giant reactors to power them) will probably not exist until there is a way to efficiently remove all that heat. Hitting something with a pulse laser is going to blast a hole in it, maybe destroy some piece of equipment. But warming it over with a beam laser is going to tax its cooling system, raise temperatures, and kill off all those handy dandy microbes in the recycling system, and then that ship is in trouble, even if they beat you off.
Vs personnel, a beam might set some one on fire. A pulse might blast a chunk of skin off. Lasers work really well when they can turn something into steam.
Carrying around a laser that is capable of doing much to armor is a problem. That industrial laser was just that: industrial. I don't think anyone was going to pick it up (and its power source!) and tote it onto a battlefield. You make a man-portable laser, and it's not going to have much energy. You might decide to spend your 50kg battery on a single shot to get all that megajoulage on one target, and that might be a whole megajoule or something. Hope no one SHOOTS your power pack. I wouldn't want a Mj exploding in MY hands.
Plasma and fusion are certainly way-cool, but you will probably never be able to fire them outside a battlesuit of some sort. All that HEAT, baby! You're going to roast yourself pretty quick. Control of magnetism and gravity probably aren't going to do much for heat you're holding in your hands. You need protection from it.
Lasers will play a part in specialized operations, like sniper ops, where you need a long range, highly accurate, nearly undetectible shot against an unarmored target. I really don't see them entering a soldier's hands any other way. Gauss guns and CPR guns are likely to be with us for a long time.