Never buy anything from the depot, the CE prices are a rip. But missions are worth doing (at least some) especially if you want to do JK runs over and over since it allows you to skip straight to the JK levels through a mission rather than doing the 5 levels before them.
Good question, I used 5 FSC runs' worth of energy on missions. Personally missions are fun, but as Trige said it *might* be worth doing missions till you unlock Royal Jelly mission.
I think the mission "Rise or Fall" (the arena mission) is more profitable than the Royal Jelly mission. You get 3-3.5k crowns, and you also get some good materials: Monster Bones and Bushy Tails. A group can do the entire mission in under 15 minutes.
With the Royal Jelly mission, it seems like you get about 2.5-3k crowns, and the materials aren't as good...
Granted I haven't unlocked those missions yet so I have no idea. But from your statement... guess I'll have to unlock the mission and test it myself.
Royal jelly also nets you tokens which you can turn into items to sell, no idea how antiguas/sealed swords are running, but I made ~18k off a catalyst after unbinding fees, so if it is anything close to that its a little over 2k per run in token value ontop of the 2.5-3k you are getting in pure crowns. Although I will admit I find selling things to be annoying.
RJ runs are repeatable. I'm pretty sure doing the missions again will mean you don't get the rewards specific to the mission, but you'll keep crowns earned.
It will probably be more worthwhile to repeat an Arena mission, if it's a t2 version of the Arena.
(I personally have not gotten to that mission yet, although I had full clearance to all tiers before this shenanigans.)
With regards to RJP, the Brute Jelly items obtainable from the tokens sell for a respectable value per item - I think it might be around 4k, and you can flog off Antiguas and Sealed Swords for a decent price if you're willing to pay unbinding fees. The materials are also sellable. Although originally they were worth a minimal amount due to the fact that people were commonly farming jelly, this may increase, since people are switching to completing missions for the time being, and since crafting is part of some of the missions available.
Also, buying the equipment for pure energy is stupid, since the prices are inanely high. If I were you, I'd just craft with the money gained.
Farm JK for things. It's far better to craft up what you need than to buy it from the depot.