Well, I missed my chance at the 40k CE and all in that crazy thread, but I've been thinking hard about what's wrong with the CE situation for a week or two now and I'm going to put down my ideas.

Spiral Knights is almost identical to Puzzle Pirates in the currency, yet SK has huge player outcry about CE and YPP has only the occasional mutter from a newbie or when the price goes up (as it does occassionally depending on ocean activity, the real world economy, and of course, new releases). So, why the difference in acceptance and what can SK learn from YPP?

1. No 'free' activity. You can -always- pillage in YPP among a variety of other activities that I assume the devs are familiar with. (Direct challenges to other players, parlor game of the day, crafting puzzle of the day, &c.) Doubloons are only needed to unlock gear and premium play activities, not basic play. As popular as it is to suggest, I don't see a way for Spiral Knights to fix this at this point. The parallel would've been to have a 'Tier 2 badge' and 'Tier 3 badge' to unlock later content instead of having consistent prices for elevators.
Different elevator costs for different tiers could be considered, but there will be more outcry if the crowns-per-CE is not greater at deeper depths - there already is some complaining at the small difference in award - lower strata are a larger difference than deeper tiers and all that, increasing difficulty is already only slightly rewarded - and mostly by materials and tokens not by crowns. Different elevator costs still wouldn't give a 'free' activity but it would give more play time for T1 players, the same for T2 players, and less for T3 players, in loose parallel to other games 'pay to unlock premium areas'.
Having some sort of totally free PvP option would be one solution to providing 'limited free activity' to keep players around, perhaps a no-prizes no-betting no-ranking variety of PvP for free. Obviously, SK chose a 'limited time' rather than 'limited content' model and so it won't work to provide too much activity as running out of ME is a motivator to buy and sink CE. The advanced training hall is a small step in that direction, but isn't really 'free play' so much as 'tutorial area.'

2. No need or desire for crowns in SK, plenty of desire for pieces of eight in YPP. It seems like CE rises in price endlessly. Though it is nearing the ceiling of 'not profitable to run on CE' now and that should cap it off. However, there's simply no good reason to sell CE. Crowns are largely unnecessary unless you are just starting. In YPP, you see costs in pure doubloons very rarely (only badges to unlock content, really) whereas you see many things with split costs; there are people constantly shifting their wealth from one form to the other to meet whichever half of a cost they don't have. In SK, you see costs in pure energy for -everything- that is a recurring cost (slot upgrades, heat amplifier, gates), as well as a pure CE cost for guild creation. Even in crafting, the crown component is trivial compared to the CE component. There's little in the way of crown sinks other than the market fees (auction and CE), so crowns are increasingly plentiful and there's very little motivation to purchase crowns from other players.
It would help if slot upgrades and such had a mirrored crown & CE cost; it would help greatly if unbinding and PvP costs are pure crowns or both crowns and CE. It would help greatly if crafting costs were adjusted again and the CE portion reduced in favor of raising crown and material costs.
Materials are almost a separate issue, but... Brinks greatly reduces the utilization of the auction house. Players who have been around any amount of time have the tokens (unless they've been selling token-bought materials to the auction house all along) to simply buy from brinks any rare or expensive material. Surely -someone- buys high-end materials, but really... high end materials are going into steady decline. Whichever ones are actually rare, will be supplemented by players acquiring them from Brinks directly or for resale at the auction house. Only low end materials are used in quantity, so, in short, there's steady market pressure down on material prices. Removing Brink's materials or increasing their costs would help create a need for crowns to use in the auction house. (Except that auction house fees are high enough that any item that reaches -truly- premium prices is going to be traded on forums or channels for CE and not in the AH for crowns.)

3. Market volatility - the CE market is -much- more volatile than Puzzle Pirates, due to several things - this is younger game ; there aren't as many people interested in selling CE (see 2) ; there aren't as many speculators filling the market demand when final purchasers aren't actively posting offers ; there aren't as many people that post offers rather than simply hitting 'buy crowns' or 'buy CE' ; and, of course, everyone who can afford it goes to craft newly released items shortly after release.
Part of this is an interface issue - in YPP the amount of Pieces of Eight you'll get for selling a Doubloon is shown, in SK, to be a speculator or even confidently use the market as a CE seller, you have to pull out a calculator and figure out what'll be left after paying a 2% fee. With that amount displayed, it would be instantly obvious when there was a 100+ crown gap ... and there would almost never -be- a gap anymore with people filling in with resell bids to close the gap. Without a gap, market-manipulating speculators can't profitably press the market by 100+ crowns with their first set of bids, they'd be throwing their profits out on their first push.
Everyone crafting items shortly after release can be offset somewhat, if an incentive to purchase CE (such as Rose Regalia or the Starter Kit) is released at the same time, or, perhaps 3-5 days after the release of new equipment as many players are starting their 4*-5* craftings. Of course, under the original crafting costs, this crafting rush would be less destabilizing, and if the crown crafting costs were better balanced with the CE costs, a crafting rush wouldn't be destabilizing at all.