A manip-less plasma generator has the advantage of being buildable for cheap, and in large quantities, without relying on highly dangerous and volatile production facilities that are best used for something else. It isn't going to be useful for a ranged weapon, as the self-contained plasma ball is exclusively a manipulator-enabled feature, but what I want to do with it is make a CQC weapon for extreme armor penetration, for our larger exosuits, battlesuits, and theoretical larger mecha. Plasma is about the only thing a synthflesh monstrosity like the Avatar of War is really vulnerable to besides powerful space magic, so having a weapon that can, provided you can actually close the distance, literally punch a limb off the thing, would be very helpful.
It also has a very secret use that I won't try to go for unless I succeed with it.
As for the FEL, its
secondary advantage is being more powerful and/or efficient than standard lasers, at least once it warms up, as well as being able to cycle the beam inside the lasing chamber to build up power. Its
primary advantage, the way I see it, is being able to fire laser beams all across the EM spectrum, from microwave to X-Ray, enabling a number of different uses besides "heat this spot up till it melts". At least part of it is non-lethal, like low-power infrared or microwaves being used to deter civilians, and some of it is purely side-effect territory like using visible-light frequencies as a big-ass nuclear-powered flashlight bright enough to sear your skin off, but some can be used for unique purposes, like wide-angle microwaves that will wreck havoc on any metals and absolutely wreck any fine electronics, or X-Rays that will deal massive critical damage to living organisms (that are partially transparent to them) even at low power that won't harm machinery as much.
Its tertiary advantage is being heavy and sturdy enough to brain a mastodon with it (its primary part is a thick block of magnetic metal segments), but I tend not to advertise it that much.