Limited vanities have increased in value exponantionally in the last year mainly because of following 2 reasons:
1) Playerbase explosion (aka Chinese invasion) -> Demand for the items increases significantly, increasing its price
2) Yen inflation -> More Yen in circulation means that items without static prices go for higher prices.
The playerbase explosion isn't something that can be fixed. So Yen inflation NEEDS to be addressed.
Look to where the majority of the Yen is generated (Be it berry to NPC selling, gym leader rematches, e4 runs, w/e) and adjust those methods fairly.
Increase the money sinks from gameplay activities such as shiny hunting to be on par with competitive play.
The main idea is to reduce the amount Yen coming into the game while increasing the amount of Yen going out.
This will make the Yen worth more over time.
It will not be an enjoyable change for many players, because it's going to become more difficult to obtain currency and it will leave your pockets faster.
But in the long run, it's the only way to save the Yen from inflating any further.
To address JJ's suggestions:
1) Money Ceiling doesn't work because alts.
2) Reintroducing time limited vanities has no impact on the Yen inflation and would only hurt the credibility of the devs.
3) Lootbox system is terrible, let the player decide which event vanity they want to buy rather than rely on RNG.
4) Increasing tournament rewards is definitely needed, as competitive play is the most Yen-sinking and canon activity of the game.