Stevedog13: If any class can use any skill or weapon then why bother with classes to begin with? I see the point you're trying to make but it just seems overly complicated. Why not simply remove classes entirely and instead give the player some "seed" points up front that they can use to buff a few skills or traits of their choosing? Then from there they can play the game using whatever skills or equipment they choose. This solves the problem in the most roguelike way possible, if you find a piece of equipment you can't really use it is entirely due to choices you made during the game and not some arbitrary rule. Who decided that I can't be a heavy armored archer who summons monsters to fight by my side?
For example, let's say I play as a Sorcerer class and along the way I find a trap set, that is a trap that can be picked up and set by the player. The Sorcerer can't use traps so I leave it alone to save space. Then I find a secret door and it leads to a treasure trove of items, but they are all high quality trap sets and special daggers. Since I am a Sorcerer I must leave empty handed, knowing that the Random Number Generator will never give me this kind of opportunity again. In a classless system I could make the decision to either continue down the Sorcerer path or switch to becoming a Thief or Trapper character instead.
Theme or gimmick dungeons might be fun as a random side path. Like maybe you find a strange looking door that gives you a funny feeling. Going through the door takes you to a smaller dungeon, perhaps only a single level, where the rules are different and allow you to do things normally not allowed in the game. Once you finish the level/dungeon you are taken back to where the strange door was but now it's gone. The player can choose to go through the door and experience the other world or simply pass it by. So long as the game is not balanced in a way that the player basically has to go through every strange door they find, then that would be fine. Balancing game play around gimmick like this, or the Undo button, completely destroys the game balance for players who don't choose to use it.
The situation in Torneko: The Last Hope isn't "any class can use anything"; it's more like:
* There is one class that can use nearly any item in the game, but doesn't get any skills or spells.
* The other two classes are limited in what items they can use, but can use skills or spells, some of which are quite powerful, but which also have their drawbacks (skills make you hungrier, spells cost HP, for example).
The result is that you have 3 classes, each with very different gameplay. Warriors work best in melee, as they don't have any ability to see down a hallway (although you *could* shoot an arrow down a hallway if you like, of course). Mages, on the other hand, should not allow any enemies to attack them, as doing so could lead to a quick game over (I even had an enemy kill me twice in one turn).
As for theme/gimmick dungeons, I was thinking more in the context of the way a Japanese roguelike is typically set up. In Japanese roguelikes, there is a town area, which is not part of the dungeon and does not behave like part of the dungeon; in particular, you don't fight enemies, you don't get hungry, you don't run into traps, you don't perform the actions that you would normally do inside a dungeon, and so on. To put it another way, towns could be seen as not really a part of the game proper. From town, you go into a dungeon, each of which is self-contained. (You can typically take items, and in some games, your level, into these dungeons, but that's a comparatively minor detail, and is not always the case.) Hence, a gimmick dungeon would be like playing a different game with the engine; in a non-Japanese roguelike, the closest equivalent would be the game asking you, when creating your character, which dungeon you want to explore.
(By the way, there is one rather interesting tradition in Japanese roguelikes; nearly always, there is a 99 or 100 floor dungeon that does not let you take any items into it, and which forces you back to level 1 (even in games that normally let you keep your level); in this dungeon, nearly any item in the game can be found. In the Shiren and Torneko games, herbs and scrolls, which come pre-identified in other dungeons, are not initially identified in this dungeon, making it feel very much like a traditional roguelike.)
The way such theme dungeons would work, then, is that you choose to go into one at the start. If you are playing a Sorcerer, you might choose a dungeon that is specifically designed with the Sorcerer in mind, designed for you to make use of the Sorcerer's strengths, but still having to be aware of the Sorcerer's weaknesses. In this dungeon, you would find only Sorcerer equipment. On the other hand, you could instead choose to play the main dungeon with this character, in which the full range of items and dangers normally present in the dungeon would apply.
When it comes to game balance, each dungeon would be balanced in isolation; the existence of a theme dungeon would not unbalance the main dungeon. If there's a dungeon where you only get wishes, the inability to take those wishes into the main dungeon would prevent it from breaking the game. If you want to have fun with wishes (basically, you controlling the treasure you get instead of the game deciding which treasure you get), you play the wishing; if you prefer the random treasure typical of roguelikes, just play the main dungeon. (I note that in the Japanese roguelike case, a gimmick item *can* be taken out of the dungeon, but depending on how the game is set up, you might actually have to play a fair portion of the dungeon to do so.)
When it comes to classes, I think I prefer having a small number of classes that follow completely different rules, rather than a large number that just differ in tweakable parameters.
The Undo button idea is just a random idea I had that, if implemented, would completely change the gameplay. On the other hand, perhaps the game has a puzzle mode, perhaps along the lines of Fay's Puzzles from Shiren the Wanderer; each puzzle is hand-made by a designer (rather than being randomly generated), and you have to use your knowledge of the game mechanics to clear the puzzle. Perhaps an Undo button could be implemented, but have it *only* be available in the puzzle mode. (After all, I notice that the DROD series (which I really should try playing one of these days) has an Undo button.)