[eluser]xwero[/eluser]
i guess you mean system/libraries. The difference is that in the system directory some of the libraries are being used by CIs core. This also means you can extend your libraries like you would do with CI libraries.
Another benefit is if you use one CI core to power multiple apps you don't have to copy libraries to each app.
From the previous you would think placing libraries in the system directory is the way to go but you have to decide for yourself if the library belongs to the application or if it's very likely the library is going to be shared.