While I know this isn't Nethack, and these are well crafted dungeons, I think there needs to be more randomness in dungeon instances then there is now. By that I mean, levers and trap location and type, type and location of certain monsters, even those puzzle squares should be rolled on a pre-generated chart much more often than it currently is.
For one thing, this game content is designed such that it is inevitable you will be replaying content. Even if you are VIP and favor isn't an issue for you (which it still might to unlock a couple of things anyway), there is still the issue of leveling, unique loot and just being in a game group that wants/needs to replay the same content. Having random elements to the dungeon will greatly increase replayability and random changes will keep you on your toes and leave content more interesting longer.
Secondly, this would slow down zerging, much more than any dungeon alert system ever could. If players can't know before hand whether that room they really bypass really is optional or whether it has a critical lever, or where the exact location of the trap and/or trap box is, or even whether the trap is fire, acid, or spikes, or whether the next room contains fire elementals, earth elementals, or stealthed wrights, suddenly players have to slow down a bit to think things out. I don't think I have to mention the benefits of slowing down zerging would be, from helping newer players enjoy the game more to reducing lag.
And on a related note, more player choices in the dungeon quests would also be nice. Stuff like do you go in room x just in the nick of time to save the prisoners from zombification, which gains you valuable ally later on, but gives time for the lieutenant to slip away, or do you kill the sub-boss in room y and find a valuable key on his body that will allow you to bypass several torturous traps, but in doing so fail to rescue the prison in room x? A minor example where this was done was "Come out and Slay" where you choose which faction to ally with if at all. In long chain quests though, you can probably have some far reaching player decisions, which would do much to increase replayability and keep limited content new.
Anyway, the quests for the most part are well designed, but I think they can only be improved by more dynamic content, especially considering the need to often repeat the same content.