Looking back, I think I struggled with Pylons' lack of convention (or perhaps flexibility) more than anything else. There seemed to be a lack of consensus (or as I saw it, no established "best" solution) for handling common middleware tasks such as user authentication. It seemed like I was spending more time on application architecture than fleshing out a working system.

This was over a year ago, and I'm sure some things have improved, but looking back into that Pylons Cookbook still gives me the willies.