Once you fly over the Nazca Lines, there's not much else to do in that region. Arequipa, however, is an interesting enough city to spend a few days in, even if you don't go to Colca Canyon. And people do take day trips to the Canyon, but I wouldn't. It's a long haul and a lot of driving/riding. Here's a review of the best hotel in Arequipa if you decide to go.

There's also a Sonesta with an awesome location right on the square and it'll do, but it's pretty disappointing apart from the view of the church from the dining/drinking balcony.