We’ve never stayed in Sedona. We like the Little America in Flagstaff. I’d stay where you plan the most activities. Sedona is very scenic and upscale and Flagstaff has a little more of a mountain/college town vibe but is still pretty.
Another consideration is that on a nice weekend in the spring, traffic through Sedona and into Oak Creek Canyon can be backed up for miles. It won’t be a quick trip up to flagstaff and back at those times.
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