I'd like to suggest that the mission reward recipes be replaced entirely by a special alchemy machine located in the Spiral Knights HQ (formerly known as the Hall of Heroes) similar to the Krogmo and Sanctuary alchemy stations. Whenever the player progresses in rank, as our helpful supporting NPCs are chiming in on other matters of importance they'd inform them as an aside that they've been authorized access to new gear. One could then visit this machine and craft it without requiring any recipes to be learned.

As for other low-end kit such as the early (or even the entire) Breaker line, the machine for that could be located in the Bazaar. Creating or upgrading one's equipment would not cost any energy but instead require very limited quantity tokens that are sold daily by a nearby NPC and granted as mission rewards. You would still need the usual materials but no added crowns. New recipes would become available as the player progresses in rank and higher end gear would require stronger mist charges. The player could then choose what line of gear they'd prefer to make as their reward without costing them playtime or cluttering them up with crap recipes, increasing the use of kit such as the Bolted Blade or Thwack Hammers or even the otherwise worthless Cautery Sword. As is, players may not even be aware of their options seeing as recipes are scattered everywhere. A separate line of recipes could be used with any normal alchemy machine, instead requiring the usual investment of energy to allow people to mass craft low-end tat for their PvP needs.

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As an aside, I'd like it if you actually upgraded your existing Proto weapons as the flavor text suggests as you use the machine. First into Bolted/Charged for the mission, and then a sidegrade into an element of your choice should you want to spend the materials. The end product doesn't need to be higher tier if no energy is expended.