If I were you, I would spend more time west of the rockies, where a lot of spectacular scenery can be found. Since you have 3 months to complete the trip, you will have plenty of time to stop and visit areas of interest along the way.

You definitely do not want to miss out on Zion and Bryce Canyon, especially since they are so close to the other areas you mentioned. You could drive up from the south Rim of the Grand Canyon (or North Rim for that matter) and stop at Zion and Bryce Canyon enroute towards Arches, Monument Valley... etc, drive north along Highway 12, a very scenic drive, and cut across Capitol Reef towards Hanksville.. Then you could visit Arches and drive south to Monument Valley and then on to Mesa Verde and southern Colorado.

Check out these photos of the areas I mentioned if you're interested..
http://community.webshots.com/user/nhippenmeyer

I'm not that familiar with the landscape east of Colorado, but I'm sure you'll have a lot more fun exploring the south-west than the great plains..

Nicholas