Why does Flash need to be able to access system files in the first place? Oh, that's right, Web 2.0. Hmmm. If a web application cannot be built without needing to access system files, then it's not a web application ... its a system application that uses web delivery.
This is a perfect example (among many others regarding Flash and even Java) of why there should be separation between web applications and traditional applications. Since the underlying OS is largely responsible for maintaining security, applications that build on that must be able to ameliorate security issues that the OS does not deal with, or which are not security issues, when run in any other scenario (i.e. running a localized app).
Clickjacking is not quite as simple as the examples given above (i.e. different href value than the displayed link value), and enabling such behavior by including system-deep access for a third party, web-deployable app is bad practice. Just because Adobe wants you to be able to access the system to increase the perceived value of their little toy* does not mean that it's a good idea.
*I've been programming with Flash since it was in virtual beta (FutureSplash), and the directions it has taken under Adobe's guidance is disturbing and unnecessary.