More variety from run to run would help to keep the game feeling fresh over the long term. But each run already takes well over an hour, so simply adding more stages would be sub-optimal.
So instead of just lengthening the game, I suggest a system of branching paths in each run. In the future, as content is added to the game, eventually each act could have one (or more!) alternate versions, and the game would randomly choose one when you go through the portal to the next act. (Alternatively, the players could choose from multiple portals.)
Such a system could help keep things fresh over the long term, without inflating run times.

