I think it would have been cool if Arizona's capital remained in Prescott. The territorial capital bounced around a few times, from Prescott to Tucson to Prescott. Tucson was the largest city at the time, but it wasn't the most desirable because of strong Confederate and Mexican influences. The southern part of the territory sided with the Confederates so it was decided to establish the first capital of AZ in Prescott.
There was a proposal to have the capital placed in La Paz county along the California border and at the confluence of the Salt and Verde Rivers which would be in present day Tonto National Forest and Indian Reservation lands.
That would be cool (the Prescott idea, not the La Paz one ).
My outsider perspective seems to think that Phoenix is a near-perfect location for the capital, but if locals think that Prescott is better, more power to you!
Prescott is geographically centered in the state and the physical setting is beautiful, however Phoenix is population centered. 85% of the state's population is metro Phoenix and south (including Yuma).
I don't think the Mississippi shifts that dramatically, although there are quite a few spots where the river has jumped the border. It's worse in the lower Mississippi where it's flatter and the river meanders a lot more. The terrain view highlights just how poorly located Kaskaskia is, right in the middle of the flood plain, and also reminds us that the Mississippi isn't a completely wild river like the river in Peru in that gif. You could see the levees protecting Kaskaskia and keeping the river contained in its current path.