Over the past 3+ decades, I've used nearly all the clipless pedal systems available. The original Look system was my favorite on the road until 5 years ago, or so. My mountain bike still has Shimano M737 pedals that are probably close to 20 years old now.
For touring, I prefer to be able to get on and off the bike without thinking about my footwear...I'm on tour and there's so much more to it than just riding all day. So I've settled into decent quality MKS flat pedals
http://www.halfords.com/webapp/wcs/stores/servlet/product_storeId_10001_catalogId_10151_productId_919607_langId_-1_categoryId_273937, the most recent pair purchased in the middle of our Wales tour in the summer of 2012. In the past few years I've toured in Crocs and these trail runners
https://www.salomon.com/us/product/xa-pro-3d-ultra-2-gtx.html.
I've not had any problems with my feet, knees or hips using these relatively flexible shoes. They are stiff for running but much more flexible than SPD-style shoes.
During our upcoming year-long trip, I'll likely start with the trail runners and replace them, when needed, with whatever I find along the way...most likely a light-weight low- or mid-cut hiking shoe.
Ultimately, choose which shoes you prefer to ride in and enjoy the ride.
Jay