A lot of dungeon features are currently fairly interesting/novel in the early game, but by the late game, are extremely inconsequential. I'd like to propose that certain features get swapped out with high end equivalents to make the endgame more interesting. These are only suggestions, of course. As a general rule, though, I'm trying to make these have a sort of parallel difficulty to their early game counterparts--eg. ant colonies are moderately difficult, so replacing them with something that produces doppelganger kings would not be appropriate since doppel kings are much higher difficulty monsters for an endgame character than ants are for an earlyish game character, proportionately speaking. Generally, I am thinking that these things should appear in late game (DL 30+ areas), possibly excluding a few areas (DH, notably). Note that DL 30+ does mean that the upgraded traps would appear in the lower levels of the Maze, which I think is kind of cool with the general increasing difficulty of the Maze, but that could be another excluded area, I suppose.

Daemon gate - replaces beehive in high DL areas:
Spawns a number of experienced fire/water/air/greater daemons. This could possibly be destroyed by kicking (say, it's a stone structure that summons daemons), but it doesn't need to be. I'd kind of like to have some small reward for finishing it, maybe just a couple of extra random items or something, but not necessary.

Elemental conflux - replaces ant hive in high DL areas:
Spawns a number of experienced fire/water/ice/air/earth elementals (and maybe a few greater ones). I personally like the idea of both this and the above producing random types of elementals/daemons, but an alternative could be to have each portal produce only a single type. I like random types better because the former way is basically just an extended threat room.

Healing spring - replaces pools in high DL areas:
Drinking from the spring completely restores HP and PP. Runs out after a certain number of uses (1d8, say). This one is kind of a freebie, but I think it's something that players would appreciate encountering. I think removing pools from deep DL areas is okay, since players rarely use them in the endgame. This could also replaces forges, I suppose.

Enchanted forge - replaces forge in high DL areas:
Smithing success rate is greatly improved. Small chance for adding random prefixes/suffixes. I'm torn as to whether adding affixes is necessarily a good idea or not, but I think having it only available in high DL forges is one way that could make it work.

Abandoned shop - replaces random gear shop in high DL areas:
A random shop's inventory is simply lying on the ground for the PC to pick up. Gives the same "abandoned shop" message as mimic tension rooms (and mimic rooms should not have the tension message anymore). This is another freebie, but so are shops generally, and it's not like gold is such an issue that you couldn't buy out an entire shop's inventory in the endgame anyway.

Tainted plants - replaces herbs
Increases energy cost for crossing them. Stepping on a tainted plant can corrupt, pierce the PC with thorns, or some other effects. Follows normal herb growth patterns. Could introduce a whole new generation of herbs, otherwise, I think picking them with herbalism could just give messages like "You pull the tainted vine out of the ground"; "You try to pull the vine out of the ground, but its roots are too strong"; "You try to pull out of the ground but only manage to prick yourself with thorns"; "A creature under the plant sudden springs from the ground! (+spawn shambling mound)"

Upgraded traps - replaces existing traps:
Light trap -> Paralysis trap (Inflicts 1d(DL/2) turns of paralysis)
Acid trap -> Noxious gas trap (Inflicts damage + heavy poison + possible sickness)
Teleport trap -> Ceiling trap (Same as usual)
Pit trap -> Spiked pit trap (Massive damage + Bleeding!)
Viper trap -> Shallow grave (Fall into pit, spawn a group of vampires)
Fireball trap -> Elemental trap (Explosion of random element)
Alarm trap -> Magic trap (Drains a massive amount of PP, chance to Mute, removes all active spells such as Strength of Atlas, Bless, etc.)
Arrow trap -> Eternium arrow trap (Big damage, scummable)
Corruption trap -> Chaos trap (Corrupts, teleports the PC, plus chance to inflict random status effects including Blind, Deaf, Mute, Stun, Confusion, Poison, Sickness, Slow, Paralysis, Drunk, etc.)
Water trap -> Water pit trap (Replaces the tile with a river tile, PC falls in and takes drowning/water damage as appropriate)
Spear trap -> Destruction trap (Effect of wand of destruction centred on PC)
Stone block trap -> Enervating trap (Random stat drain)

Upgrade door traps - replaces existing traps
Exploding rune -> Fine as it is
Collapsing door -> Death ray trap (Chance to death ray* if the PC is standing directly in front of the door)
Stone block -> Living wall trap (Instead of a stone block, a living wall falls on the PC; if not dodged, PC take damage, item destruction as usual, and has to fight the living wall)
Booby trap -> Elemental trap (Random elemental explosion)
Stunning rune -> Gas trap (Causes PC to fall asleep for 1dDL turns unless resisted)
[*]I dislike having random instakills due to death ray/petrify in general, but I do think these effects are grossly underused. Since door traps are quite easy to avoid, and this trap can always be safely avoided simply by standing diagonally to the door, as well as by dodging or whatever, I think this is an okay way to put it in. I was originally planning to write this as a petrify trap, but death rays already have a precedent for being directional and petrify resistance is quite a bit rarer, so I thought death rays would be more fair.

Upgraded rivers - see this thread for some ideas

Royal treasury - replace the gold with some more interesting loot (not sure what, precisely, maybe random loot or just random weapons/armor like Darkforge or something), add some extra royal guardians in the room.