I would like to see some sort of story attatched to other events, i.e. the fall of an overlord unlocking a large chunck of the mysteries, the puzzle rooms are quiet an amusing distractions but considering the number of required to get through even one mystery, it is quite an uphill strugle. If possible id like to see a central mystery focused around the objectives, such as lietuneints falls or advancing to the next tier, by doing this we could have a bit more background, while using the mystery rooms to give a better back story.
For example you could tell the tale of a legendary glyphbearer in the mystery rooms or any other side content, while the main story of the cataclysm is proactively unlocked through your normal actions.