You absolutely must go to the Museum of Northern Arizona, just outside of Flagstaff. It has two wings - one for the natural history of the area and one for the cultural history of the area. They often have hands-on activities, demonstrations, and a couple rotating exhibits. Do the museum *before* heading out to Walnut Canyon, Sunset Crater, or Wupatki or even Camp Verde/Montezuma's Castle & Well.
While you're on the Museum side of town, drive up to the Snow Bowl and walk around some of the trails to see the change in vegetation w/ altitude. Merriam of Merriam's Life Zones spent a fair bit of time in AZ. The trail up Mt. Humphries begins at the parking lot. It is a challenging, but doable climb. There's nothing like being above the timber line. Nothing in the world! Take good shoes and water and a wind breaker for up top. And do this as early in the morning as you can manage to avoid afternoon storms.
If the peak isn't your cup of tea, may I recommend driving up the other side and picnicking (or camping) in the Inner Basin. The drive is a little hair-raising but worth it. (I wouldn't take an RV up the first time...)
The most interesting wildlife is found on San Francisco Street downtown. Shopping is good. Restaurants cater to the college set... and the hippies. Lots of vegetarian fare.