Actually I can relate. I am recovering from a minor knee injury and for some reason, I can't ride clipless right now. Clips and straps are much more comfortable, whereas Clipless bothers my knee. I have no idea why. As for shoes, I used to ride with chucks in clips and straps but just got myself a pair of Asics (link at bottom). They are WAY better, they feel snugger in the clips, while being just as easy to pull out and have a lot more support so are much better for walking too. I tried some Adidas indoor soccer shoes which were pretty comfy but the Asics won by a mile for me. Plus I like the colour. (They do come in other colours)

http://img.player.co.kr/goods_img/13209/13209_392.jpg