Integrating applications to OS is something that Microsoft has done with IE. Parts of the browser are pre-loaded to memory during OS startup and application start times are faster than with competitor browsers etc.. As such Skype is just an application that is integrated to contacts app and phones IM/VoiP framework. E.g. Fring plugin should be able to behave exactly the same with same performance, or there are some design flaws in the OS and built in applications.

The fact that Skype comes pre-installed and integrated to existing device functionality doesn't and shouldn't mean that it's integrated to OS.