There has to be a mechanism for the PC's to advance the plot. Both Keeper and player prefer games where the players do so on their own initiative.
I think it's interesting to suggest that some non-core clues are passive pickups (You have a high Architecture skill, you get this clue) while others require you to act in some way.
Whatever system is in use, I think it's important for the players to understand what the DM/Keeper is doing. If, for example, I know I'll pick up some clues just by virtue of a high skill, I can play with the assumption that my 'detect architecture' skill is always 'on'. I'll know to ask for specific or esoteric things, and that I'm going to get to roleplay a lot before making a Diplomacy check.
- "Don't assume you are safe because there is a rational explanation for all of this."