The problem with mountain running vs a 100k ultra is that it is more specialized - both in terms of terrain and skills. You could have a looped ultra trail course in a lot of places but for mountain running real mountains are required. Also, it should not be so difficult that it becomes a freak show like the Barkley course. I think a goal should be to open up the sport to top runners that have not been attracted to ultras previously. A 100k ultra that is somewhat technical but not so extreme would be the best middle ground. At the end of the day the Olympics should be about competition between the best athletes and not just between competitors willing to endure the most discomfort in extreme conditions.
The other thing that would increase interest would be to award team medals and score it like an xc meet. Imagine having a Kenyan and Ethiopian team battling it out with American, Chinese and Japanese runners. That would also keep interest high until all the runners came in for the top teams.
Yes, I know it is unlikely to ever happen, but we can still dream, right?