I agree with what everyone else said. I've run both twice in the past 3 years. I think the people you go with is more important than the trail. That being said, the scales tip toward the Rubicon for me. Granted, there's more liability - driving 1000 miles out there, wheeling for 2-3 days over tougher terrain, and then driving back home, but I prefer the Rubicon trail for several reasons.
If you want a challenge, the Rubicon is more challenging. If you want Utah History and desert terrain, HITR. I prefer the pine trees and all the lakes of the Rubicon trail. I don't have any plans to run Hole in the Rock again in my life, but I can't say the same about the Rubicon. I will be back, even if it's just to backpack the trail.
[video=youtube_share;GmdmR8W5Kk4]http://youtu.be/GmdmR8W5Kk4[/video]
[video=youtube;F8sAn8dOwUU]https://www.youtube.com/watch?v=F8sAn8dOwUU[/video]