Good article. As someone who's worked with SSIS for about a year, a lot of your recommendations rang true.
I'm not sure I concur with the one-configuration-setting-per-configuration-file suggestion however. If you have more than 10 settings...that could make for more headaches that it's worth. Add different configuration locations (database, XML, registry, etc) and that would just compound the problem. Bundling them into groups, by their functionality, would be a better approach IMO.
What's missing in the SSIS-discussion-space is a good article on utilizing the event handlers. To be honest, I've ignored them but would like to see how they could effectively be used.