This is a good question and I've seen it done both ways. There's definitely reasons Not to include the CI files. Like any potential in the future license changes. And it seems like with the projects that are shared by more experienced developers that is how they do it.
Because if you are sharing your project for other CI developers, then the reality is they will not use the copy of CI you include - they will fold your files into their version of CI. So including JUST the files needed for your app - actually makes much it easier. Its certainly what I would prefer. Just keep the standard application folder structure: config controllers models etc. but only include the folders that you have files for. And make it clear what version of CI you have tested it on. If you can say it will work on the release version (not the beta) then people on PHP 5.2 will know they can use it.