I guess I can't imagine traveling hundreds of miles for the main purpose of the Grand Canyon and staying in Flagstaff and day-tripping one day to the Canyon.
It would be so much more relaxing to stay right at the Canyon at Trailer Village if one wanted full hookups or at the lovely Mather campground if the RV is small enough and you didn't need hookups. Desert View on the East end of the Canyon is also a nice dry campground. I'd advise to spend at least 3 nights at the Canyon.
There is plenty to do without being rushed. Take advantage of some of the ranger programs, walk the wonderful trail at the top on the Rim Trail which is pretty flat. I'd also advise at least a 1/8 - 1/4 mile walk down the Bright Angel Trail to get a whole new perspective of the canyon from below. (Take water) Take the free shuttle and get off at various areas to explore the Rim Trail from those areas. Spend a day driving to the East section of the park. Attend a campfire program.
Yes, Flagstaff has some great Indian ruins to visit but there are RV parks in Flagstaff to explore those closer areas. Bonito Nat'l Forest campground at the entrance of Sunset Crater Volcano Nat'l Monument is our favorite. It's gorgeous. From there you could do the Volcano, Wupatki Nat'l Monument, Walnut Canyon Nat'l Monument, Meteor Crater.
If staying in Williams and taking the train to Grand Canyon, the train ride is through open scrub land and once at the Canyon you only have a couple hours at the Canyon to explore.
To tour the Sedona/Jerome area we always stay at Dead Horse Ranch State Park in Cottonwood.
There are many options.