Energy Cost, Size, and/or Charge Time.

You could have a weapon that's basically a Rocket Launcher Equivalent. The thing doesn't have an emitter built in, but instead it shoots the emitter at the enemy. The projectile it fires is basically a sticky-bomb. It attaches itself to the enemy's armor, then dumps all the power it can manage through the emitter. If you want to be fun, you can have specialized rounds for this thing.

You can have omnidirectional emitters that are designed to fry groups that stick too close together, or a sticky-bomb one that just fries the person it's attached to. Be creative here.

The problem here: It's a gun that fires guns. It's going to be big, and heavy. Training people to use it effectively is going to be expensive, and whoever's carrying it into the field isn't going to be able to have as heavy a pack since they're having to haul the Launcher and all the ammunition they're expected to need. Also: The ammo is going to be expensive to make, and even if you can refurbish the spent ammo... it's going to make logistics more complicated.

Medium Size weapons could have a standard emitter, but they could have a modified focusing system which prevents the particles from decaying. This results in the weapon being capable of "charging a shot." These charged shots would take time to power up, because you're still emmitting the same numbers of particle per second, but when at full charge they're able to punch through armor.

The weapon's light enough to not be entirely impractical, but it's still going to be tiring for someone to haul about. It's also going to be more expensive to build because of the fancy focuser, and the fact that it's going to need a larger power supply (and maybe larger crystals) to account for the fact that it's going to go through more ammo than a normal weapon. Add in the lower rate of fire, and you get the kind of gun you hand over to a specialist. Think a Scout-Sniper, rather than an infantryman.

Ship-Mounted Weapons, or Ultra-Heavy Weapons, could just be a matter of scale. Put a ton of Emmitters together, along with their Crystals and Power Supplies, in the same housing with the same Focusing Device. This thing would be like firing fifty normal shots at once. One of those rounds lands, you're dead where you stand unless you're wearing a tank. But, as usual, it has some drawbacks.

The first one is that it's going to be big. It's big enough that it needs to be mounted onto a vehicle to be used effectively. It's also probably not going to be easy to aim. This thing's a Tank's main gun, or something you slap on a ship. It's also going to be expensive to build, and to keep charged up.

Small Arms that 1HKOs people are a bit weird. You could have one of those chargeups in a pistol, but it would take a long time to charge.