This issue has come up several times in the past in various forms. With the new Native Installer options and more maturity in the tools, I'm hoping there is some defined best practices for dealing with distributing small AIR applications with large asset libraries. Developing educational tools that can not have their media content remote has been a challenge for AIR. The idea of just putting the media content in the src directory and moving on is simple at first but becomes a serious nightmare down the line. ELS doesn't work well with LARGE applications and forget the auto update frameworks. If you have a small application bug fix you have to push ALL assets with it and that is just not practical.
A few things I believe I'm looking for but would love some feedback from the community: