I never really paid much attention to the towns in the clockworks before missions, and ever since the addition of missions, the towns really don't have much of a purpose at all. I have two suggestions that don't involve changing the crown or energy costs like others have suggested.
Missions at the towns: I though it would be cool if there were missions at the towns that would only be activated until you have gone through the previous depths on that gate (to prevent just starting up on the next tier to jump to them). These could involve things such as those ghost train tracks, the desk clerk asking for something, or the dark ritual in Moorcroft Manor. This would not only make the towns more important, but also make the Arcade more worth playing.
Make the towns like Haven: It would be kind of nice to have the towns like haven where you can see every other player in that instance. The elevators could be set up like they are in the arcade. In towns, each gate will keep their crown costs if the player has not gone through the previous depth. For example, elevators in Moorcroft will cost 200 crowns and 10 energy, assuming the player has not unlocked the same gate from the previous depth, and does not have an elevator pass. This would make the towns a hub similar to Haven, maybe with some nice little extra features only available in those places, so they are worth going to (I don't have any idea what would be added though).
I like both the requirement to go through the Arcade and reach the sub-town to do possible missions in them. I feel as if that can really spark some life back into the Arcade itself.
On Sub-Town Missions: There's some real potential to introduce more story into Spiral Knights with such missions (I for one would really like to see the sub-towns either expanded or explained-- for instance, what dark ritual?). One possible type of mission (discussed in another thread) could deal with the specific stratum of the levels below. For instance, a stratum with emphasis on beasts could have some beast-related missions. Using your example of a mission with the "dark ritual", perhaps the Kat requires materials from the floors below.
On Sub-Town Sub-Havens: I'm not too keen on this idea, if just for it seeming as if it is just a copy of the Haven above. In addition, with not many people playing the Arcade, the towns might seem pretty unpopulated. In addition, Emberlight could become a hotspot for beggers and spammers, who're attracted to the T3 knights.