They have a defferent range and damage at a certain range. I can't remember witch but one of them damages 20 at range 1 and the other one damages 15 but has a longer averall range.
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The only thing I can think of is that the Plasma Bolt technology continues further than the Electric one at the highest tech levels. Basically, I use the Electric weapon until I've reached the highest technology levels - only then do I use the Plasma (b/c it's better).
Something related that I don't understand: why the name change in the middle of the technology tree? The weapons do the same thing as the lower tech ones - why not just keep incrementing the roman numerals?