Oddly, I now live in Asheville, but spent 3 1/2 years in Flagstaff and 6 months in Missoula. Personally, I love Asheville most of all. Here's the pros and cons of each:
Missoula: Smaller. High Mountains. Great winter sports if you're into that. Great beers, fun college town. Proximity to other outdoor attractions, such as Glacier, Bitteroorts, Hells Canyon, etc. CONS: The winters are mega-rough. Very little music or culture scene. High cost of living, but little lower compared to Flagstaff, higher than Asheville. Finally, in my opinion, the mtbing better in both the other two places- mostly because of the extended seasons.
Flagstaff: ( I LOVE FLAG!) Smaller. Incredible mountains and canyons. Great climate- some heavy snows in winters at town elevation, great snow pack up on the "peaks," good winter sports, but snows at town elevation melt and drain fast enough for year round riding. Sedona, 30 minutes south, will be 60-70 degrees in middle of winter, incredible canyons and mtbing there. IF YOU'RE INTO MULTIPLE SPORTS, THIS IS THE BEST AREA. Incredible rock climbing, high alpine wilderness hiking, miles of mtbing, caving, THE GRAND CANYON is an hour and half way, Zion is 4 1/2 hours, Moab 8, Durango 4, etc. There are a great deal of "secret" places in Flagstaff that you would be just amazed by (Pumphouse Wash, for example, starts as a 50 foot deep gully behind an area called Kachina Village. If you know the way in, within a few miles, it erodes to 750-foot plus deep canyon with year round flowing water, nesting eagles, and not a soul around...) This is the one place I've been (I also lived in Colorado for a while) that I can honestly say is better for outdoor sports then Asheville... also, there's a very active environmental movement in this area and the Native American arts and spirituality can be fascinating CONS: Higher cost of living than either of the other two. Very limited culture or music scene...I lived there for 3 1/2 years and exactly ONE good local band developed itself and maybe 5 good regional/national acts visited- that's pretty lousy for college town. Finally, it is primarily a college and tourist town. It's hard to make friends here because the population is pretty transient, unless you're a 23 year old bro with dreads and mad skills, or at least can act like some form of snob like that...it's just not that friendly of a place, in my experience.
Asheville: (I REALLY LOVE IT HERE!) Friendly people. Great mountains. A live, vibrant music and arts scene- this cannot be emphasized enough. Over the course of the next month, in this town of less than 200,000, at just one single venue, Sonic Youth, Blondie, Gomez, and several other acts will be playing. Bluegrass and folk music is so thick it gets in the damn way. Festivals are everywhere, with super fun acts...some great musicians like Martin Sexton, Ziggy Marley, Doc Watson, Dell McCoury, Gillian Welch, etc. can be counted to play here at least once a year , for the acoustic acts sometime 3-4 times a year, and that's not even counting the large number of mega-quality local acts... galleries abound with crafts being prevalent. Whatever your leanings, there is a spirtual communtiy that can meet your needs...even if those are none at all. GREAT BEERS. Better road riding than either of the other two. Mountain biking is at the same level as Flagstaff, except for much of the summer it's often too muddy to ride, but I also was riding in jersey and shorts in December, January, and Feb this last year- you can always count on a few 60-degree days.Good rock climbing, great kayaking, great wilderness areas, Smoky Mountain National Park, Blue Ridge Parkway Again, FRIENDLY PEOPLE. You can find something unique and fun to do every night of the week, if you were so inclined. CONS: It does rain a lot sometimes, the cost of living can be high, and you sometimes have to accept the fact that the rest of the state is super-conservative and you might not like most of what the government outside of Asheville does(unless you lean that way yourself- I don't)- but our local political scene is great for it's diversity and the fact that we do all, eventually, get along in the end.
OK that's enough for now. Flag and Asheville are both GREAT Places- FLag does have better weather and is more astonshing outdoors wise, but Asheville is almost at it's level outdoors-wise and has a better vibe. Peace.