Hello,
I will add my input from a person who has been helped numerous times by the Flex related forum (especially R. Scheitlin).
We started with the FlexViewer (over 2 yrs ago - wow time flies) and have a Situational Awareness App and a Cemetery Viewer based on it. They are still being used. We highly altered the source code to meet our needs. We had no Flex programming experience although we did have experience with various programming languages (but are experts by no means). The FlexViewer and its related source code really helped us to understand Flex. It also allowed us to have a basic web app up and running much faster than we thought possible.
The thing is that the samples on resources.arcgis.com for the Flex API are more meant for use for coding without the FlexViewer. Which caused some confusion in the beginning before we realized what was going on.
After a while, I wanted to create some simpler Flex apps without using FlexViewer so that we could really customize how it looks. Robert is right, it isn't like you can just move a widget from the FlexViewer to a non-FlexViewer app and it will work. But, you can still use the FlexViewer source code for reference to see how some code works. We now have a few web apps that are not FlexViewer based.
I would highly suggest starting with the FlexViewer and then decide if you want to move on to creating a non-FlexViewer app. By the way, my code would not pass any critiques by pro-web developers. 🙂
Carmen