The desert's dungeons (cave and tomb) are extremely hard and slow to fight through. But in comparison, they're very unrewarding. Practically there is nothing unique there except for horde of new types enemies (often respawning or overcrowding the entrance area).
I believe it should contain some unique loot or entrances to unique locations (like orcish mines at lvl.3, however, due to extreme overcrowdingness of the entrance area it's just impossible to enter :)).
The problem is also that there is some "Cap" of the player's possible level. E.g. the player can hardly beat the Tomb until he's level 15-16. Even after rebalancing the demonic chests are very hard to beat (that means fun) :) There are almost no enemies that provide leveling up further, but beating the entry location is still too hard (enemies take by numbers, not by levels). By that time all the skills are learned, all the equipment is already titanium/magnicium and Heart-Shaped-Crystals are unneeded as the player has 25-27 HP at that moment (or won't be able to get one if he has lower health).
I'm not sure how to fix the issue (it's a complex one! :)), but let me try a few suggestions:
Clearing the area near player's entry to the roguelike areas. So that there will be no demonic chest or a horde of kobolds. That will enable to enter the location easier (the locations are itself much easier except for the problem when accidentally getting into mess with overcrowded entry room).
Create some safe places inside the Desert caves for the player to rest and recover. Maybe, make it buildable again?
Remove Titanium and Magnicium from the Overworld/Cave/Dungeon/Grotto loot. Also make them uncraftable. So that they can be only found/bought in Tomb/Desert cave.
Make skillbooks different. E.g. not just a regular skillbook providing the player with +1 level of skill, but "Adept Alchemy Skill Book" which won't train player higher than "Adept" level. The best books "Master" are the hardest to obtain.
(???) Increase the prerequisites to craft best armor (we've talked about that before afair), e.g. the master forge can be found on the lowest level of the Desert caves. Or some unique resources required to craft best items like obsidian+ore = titanium/magnicium, obtainable only on the lowest level of the Desert caves.
Make player go down the hell to solve some special quests for the NPCs (like we've talked about in another issue). So that there is a reason to risk and "suffer" trying to explore the deepest Tomb/Desert Cave levels in search for some unique item or to save some NPC.
Maybe, the easiest and the most rewarding. Thou I'm not very sure about which idea you have for future... The lowest level contain a key to activate the portal (not with gems, but with some unique artifact). These locations may also be organized in terms of a very deep dungeon (and overworld's cave is a good candidate, just make it 20-50 levels deep like other roguelikes). With progress down regularly "stopped" by closed doors/portals which require getting new keys. Each set of levels should have unique look and enemies (it still might be just color-cycled of regular one) becoming progressively harder to advance. With some ultimate goal to reach the deepest level and to get (something) which either just "makes you win the game" or provides some cool ability, e.g. to reshape the world.
(ugh... those were too many words. The idea is simple: Give player the reason to go down the deepest Tomb/Desert cave level, as it's very hard to :))