Alright, there are more than enough threads suggesting how clockworks can be superior/on par with missions. I mean, it's a pretty major problem: The clockworks should be the major part of the game, and not just replaced by 1/2 farmable boss missions, after all.

However, while there are more than enough threads about making normal arcade more useful, I didn't saw a single one that suggested making longer runs on arcades more appealing. I mean: The only time you would probably do more than one tier in a single expedition is to get the achievements "Cradle and all" or "Dauntless Delver"... if you even care about completing overclomplicated achievements that aren't even worth the bragging rights you can't claim, as others can't see achievements.
Long story short: I would not only like arcade itself be profitable, but also longer runs more appealing.

And that's why I would like to suggest a new mechanic: Supercharged crowns.

Now let's just say, the spiral order has found out that the metal of what crowns are made has an ability to store minimal amounts of energy in them. Or rather, their metal can and will chemically react with the energy in the atmosphere. However, as soon as you put them too far away from an energy source(in other words, take them with you to the surface, just far enough from the core and other potential great power sources), they lose their abilitys to suck even more energy out of the air. They do, however, keep the energy they already stored for some time, ready to be extracted with special devices. They are knights, and thus they probably need the energy just as desperately as you do. So, the longer you explore and the deeper you get with the crowns you collected so far, the more energy they will store and thus, as you now have a very tiny bit of energy per crown, you basically get more crowns per crown.
... I know, there probably are some plot- and logic-holes, but it's really just to handwave how that new mechanic works.
Bad excuse aside, this mechanic basically adds a multiplier to your crowns depending on how many stratums you clear in a single run.

First off all, just a small nerf to make this method fair: In case this isn't already like this, the E-revive counter should NOT reset upon reaching a subtown. In other words, to get some profit out of this, you should do your best not dying too often, as the revive costs bottle up on the whole trip. And as you already need more energy than your mist tank can carry for longer trips, in case you aim for high multiplicators, each revive costs you your beloved CE. As reviving has different costs on different tiers, the actual death count has to be safed.

Alriiight! Now imagine the following: You want to farm some money, so you want to... let's say, you want to do a royal jelly run. It's easy, and the payout is rather nice. Okay, you go to the mission that leads you to the palace, and you clear the whole stage with boss and bonus room. Easy and fast money. It should be at around 2400 CR per run.
NOW imagine you have some more free time and you are bored. Instead of the mission, you simply go arcade... ah yeah, let's do that whole tier. You clear that first stratum. Compared to the palace, that was a cakewalk. Alright, just see wether Basil has to offer something new and then it's time to go deeper. So, you clear that run... easy routine. You get behind that boss room, "Haven"... and now it's time for your statistics. You see the amount of crowns you got: More than the mission-run, but that was to be expected after running through twice as much floors... "Supercharged Bonus x1.2"? Hey, that multiplicator just manipulated your statistic and with that, your balance, too. Awesome! You automatically made more money by just clearing 2 tiers instead of that boss-palace.
Wait, what if... go waaay back to tier 1, depth 0. Alright, time to show that tier 1 enemys your new neat pr0-$killz. Alright, stratum 1, stratum 2, ghost hotel, stratum 3... ah dang, my mist just depleted, let that trip better be worth that CE... alright, jelly palace. You show that spineless jellys that bones are hard and hurt when they hit, and after showing the same to their king, you go to that elevator and choose "Haven" again. Statistics are the same as usual... no wait! The magic number appears again. "Supercharged Bonus x1.6"? Oh my gawd, you just multiplied your payout by 1.6 for the exact same amount of energy you would need for 2 seperate runs. Or 4 mission runs. In other words, you just used your energy more efficiently... by playing longer and more than just one stage over and over again.

The multiplicator table I thought might be fine per stratum. Note: if you aren't fine with it, be free to nerf my table. It shouldn't break the economy too much, it should just reward player for playing single longer sessions. Also, you only get the next multiplicator by actually clearing the stratum: Aborting at stratum 3 will still only net you the 2-stratum-multiplicator):

1. x1. One stratum. Self-explanatory.
2. x1.1. That's one tier in total. In other words, simply doing one whole tier most likely gives you more crown per energy than a mission.
3. x1.3. The point where your mist energy is almost depleted. If you waste all your energy(-10 and everything else that already has reloaded) on a single trip, you basically get 30% more crowns that usual. I think that's some pretty decent payout, providing you don't die all the time. Otherwise you probably only get x1.2, but I think that's just as right.
4. x1.6. Basically, if you do 2 full tiers, your payout increases by 60%. However, mind you: You need CE to progress, as your mist tank is most likely empty now(2 full tiers should be 120 E). Reviving(that still gets more and more expensive each time you do it) also is only possible with CE now. You have been warned.
5. x2.0. Almost is gone. You now double your reward. However, as you need to clear at the very least 5 stratums, that also means that you have to have access for tier 3, start at tier 1 and that rev-costs STILL stack. Not to mention that progressing that far requires you to have at least 150 E in total. At least. Don't be too ashamed when you die. It always happens. Unless you have inhuman reflexes and a godly internet connection, that is.
6. x2.3. Yep. That's the full clockwork run. This is it. Minimum 180 energy to spend. Not only does everything for 5 stratums apply, but if you aim for this multiplicator in the current system, you are always guaranteed to encounter one boss. However, that also means that your payout is 130% higher than the normal one. Remember that punny areas in Tier 1 that, with some luck, could gross 1000 out each? Now they're worth 2300 each. That's nearly a full Jelly run, squeezed into 10 E instead of 30. But then again, you earned it: Everytime you died, your rev-costs stacked, so unless you never died, that rev-costs should probably have nerfed your payout quite a bit, but not enough to not make it enjoyable. Plus you actually had the time and skill to pull this one off here. Feel proud, enjoy the money and now, for Vog's sake, do something else. A full run probably is quite exhausting and expensive, so right now, just look at your great income, look for what item at the AH you can waste that money, maybe play some rounds lockdown/bomberman, and then wait until the next day.

As I said, as I'm pretty sure the multiplicators are overpowered like that, I'll just leave it to you to find a better balance. My main point is that it should be highly rewarding to do longer runs. Or rather: Doing more and different stratums in a single run, not repeating the same things over and over again.

Feedback would be appreciated. And I don't want people to complain too much about overpowered multiplicators: I already told you that you are free to think of a more balanced set yourself. i want you to judge the idea in general.