First impressions: User Guide
In my opinion, the User Guide jumps in too much at the deep end for a new user. It seems to be seasoned Drupalers and written in the style of a developer for developers (or, at least, those who have some familiarity with programming concepts).
What is needed is a really simple Getting Started / How to guide for complete Commerce beginners (but with enough knowledge to run a small-to-medium-sized, non-commerce Drupal site—something that will show them the ABCs of setting up a few products in a simple shopping cart and making it live on the website.
This would be particularly useful for non-Kickstart users who need to add Commerce to an existing website.
I thought this article by Ryan on Drupal Watchdog would be a very good starter as something like this even does not seem to be on this website.
Is it possible to copy this article, or a variation, into the User Guide?