It shouldnt matter what kind of weapon you use,energy weapon or normal, example Im using my redrix but I cant use my fav smg or my fav ar bc isnt energy weapon, and we are forced to find a good weapon that fits our gameplay again just bc of that barrier or -blam!- option
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If they did a good way of doing it would be to make whatever weapon you choose for a second slot should auto change affinity to match subclass ,so for example if it's a kinetic weapon in the second slot but your using a ark super the kinetic weapon in second slot should change to ark