That's how I always explained it away. Because of the materials used in the construction and the different sciences involved in the design process of the different types of equipment it's a good enough explanation.You could argue it has something to do with different materials being used to construct the weapons/the weapons operating on slightly different principles.
I think you guys are trying to read a little too much Tech into this.
IMHO It's clearly a Viewer Perception of who's the good guys and who's bad.
Visual Artistic endeavors from Picasso to date, have used color schemes to "mold" the perception of the viewer.
Same here. they want you to feel warm and yummy when you see "Federation" good guys, and to frown and pucker you lips, when the bad guys shoot.
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