Prescott is cool. Has many more amenities that Flagstaff, arguably better weather, too. Job market is improving, but its bread and butter is old people and rehab (addiction). It's growing fast, so housing is really decently priced for brand new units. It's beginning to feel like small town Southern California, which isn't all bad.
Phoenix has some nice areas, Cave Creek in particular. Downside is that all the jobs are in Tempe or closer to downtown. Phoenix is the type of place where you get a job, rent until your settled, then buy as near to your employer as possible. Sitting in traffic for an hour while its 120º is akin to being in a submarine a mile down or in space station. Hope that nothing fails or else you boil. Winter in Phoenix is awesome though, nothing quite like shorts and t-shirt in January. Summertime is "Exodus Season" in Phoenix, with everyone scattering for higher elevations on the weekends. Job market is strong too, with lots of employers offering competitive wages - even by California standards.
If I had to choose between Tucson and Phoenix, I'm not sure which I'd choose. Tucson has more history, for sure. It's a big city with small city feel in a lot of ways. Highest rates of unemployment in the state, though.
If I was looking for jobs in the Southwest, but wanted to be relatively close to a wide variety of amenities, housing, other jobs, outdoor opportunities, etc - I'd probably look real hard at Palm Springs, Palm Desert, Indio. It's far enough away from LA and San Diego that it's housing is still reasonable - also there aren't any colleges to make for a massive influx of seasonal renters. It's got similar weather to Phoenix, but is more compact and closer to the mountains. An hour's drive will have you in Riverside. 2hrs will have at you at the beach.
Reno is another one to look at. 2 hours to Sacremento. 3 hours to most of the Bay Area. Nevada taxes are low. Housing is well priced. Carson City, Tahoe, Truckee provide cool weekend destinations.
Albuquerque is a tough one. I really like Santa Fe, and would prefer it over Flagstaff for a few reasons, but it shares many of Flagstaff's isolation issues. Albuquerque is a seriously cool city, don't let Breaking Bad fool you, and the relationship (and proximity) between ABQ and Santa Fe is pretty close (only about 45 minutes) but New Mexico as a whole is isolated. It's a long drive to Phoenix. It's a long drive to Durango or Pueblo or Amarillo (if you ever wanted to go there) and even a long drive to El Paso or Las Cruces. Unless you've got family and a big group of friends nearby, that sense of "we're out here on our own" can get to you. You do everything there is to do in the city, then the nearest town, the nearest 5 towns, then most of the stuff in the state, and before long you realize "we're either going to have to fly or drive a really long way to explore new places." That being said, the beauty of the southwest lends itself to quite a few years of backroad and ghost town exploring before you'll get bored.