Windows Registry

Can anyone give me a good reason why applications should be allowed to modify the registry?  I mean settings can be stored in configuration files in the folder, auto run shit can go back to the route of shortcuts in startup folders.  Gimmie a reason that makes the security hole worth it.

Can anyone give me a good reason why applications should be allowed to modify the filesystem?  I mean settings can be stored in the registry, so can auto run shit.  Gimmie a reason that makes the security hole worth it.