Mix and match weapons.

[ojo de oro]

I think u should be able to change the skill of your weapon with the other skills of that same weapon type. Some weapons have super interesting passive and i think matching them with different skills would be give tons of playstyle options. most pasive/skill combos sinergize best with each other but i still think some other combinations could work great.
This would requiere the boss weapons to be given passives since they don't have any. 

[Tired_Awaii]

I think Proto weapons could be turned into something that allows you to make more personalized weapons cause as they are, they are pretty much doomed to be forgotten as other weapons can be upgraded past its max and the weapon breaking would just be a hassle.