I'll be interested in this thread. As I've returned to riding I'm concerned about knee pain as well. Not from biking per se, but in general. I've been off the bike for 2-3 years. My knees have gotten more problematic as I've aged, to the point where bending down or squatting is a bit of a challenge - especially standing back up!
These days I'm out and about in short rides on my Globe, on platform pedals usually with athletic shoes, occasionally my MTB shoes. I do notice knee pain, but it's not unbearable. I'm hoping that by easing myself back into cycling, I'll sort of loosen up my knees once again. I'm also hoping that a thorough fitting on my Masi, when it arrives, will address this issue as well.
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2015 Sirrus Elite
Proud member of the original Club Tombay