Hi Joris,
This is a really great post! Not least because it overlaps a lot with ideas I've been puzzling over for a long time.
I've not been interest in cycles for their own sake, but I have been concerned with accommodating them as part of general graph-based layout generation... See my posts over the last year or so in the group history for details if you are interested.
I particularly like the way you build semantic/narrative interpretations on top of the simple geometry e.g. ideas like having a long safe vs. a short dangerous route; long ways out that reveal shortcuts back; or traps, the reverse of that, where there's an easy way into a location, but the way back is much harder.
In terms of general graphs similar ideas can be attached to other constructs. e.g. a locked door can be reachable at an early stage, but the key is down a branch where an obstacle must be traversed... so that is putting similar semantic/narrative interpretation onto a simple T-junction (and the interpretation remains if the T-junction becomes a crossroads where the 4th direction is part of some unrelated construct -- as long as you do not accidentally short-cut something that is supposed to be hard.)
Was your figure 3 example 100% automatically generated? It's not quite clear from the write-up, but as you have a functional game prototype I assume it must be the case?
Great work!
Ian