Not sure what you mean by "lose your package layout"...I don't think I've lost any layout in the packages I've migrated to structured sotrage files and I'm using embedded packages in a number of packages. Can you expand more on that?

I agree that it's convenient to look at the logs right in SQL Server, but you can store those logs in files too (dynamically configuring the package to write the log file to a particular location). That can make it "easier" for support folks as they don't have to connect to the server to look at the logs -- although with very large log files that can become quite difficult or impossible. But then, you're not cluttering up your SQL Server with all that data either.

Limits to INI file size can certainly limits its usefulness, but it's not the only method for storing configuration data, as Phil mentioned you can use the database as well, or some other method uf you want.

I agree with Phil, I think you get the most bang for your buck with dynamic configuration, once you do that then the actual physical location of the package becomes moot, migration becomes a matter of moving your package (if you need to at all) and changing your configuration data.