Well, regardless of reality, in fiction prototypes are always better! They just usually come with drawbacks.
Often they were too costly to mass produce, and the finals are nerfed, or they even malfunction from time to time.
I still doubt they will eclipse HardLight, but, there might be a legendary energy auto rifle almost as good. Which cheapens the HL, IMO.
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Perhaps (this is just a fun theory) Hard Light is the rare prototype, but by the time TTK comes out, Omolon will have figured out how to change it so they can mass produce a final, cheaper to make, version. And that weapon will be a legendary, furthering the idea of it being able to be mass produced to guardians. All this speculation is getting really fun!