On Mac OS X, it has been considered that putting an application folder/icon in the trash (even if some other stuff might happen in the process), was a superior

On Mac OS X, it has been considered that putting an application folder/icon in the trash (even if some other stuff might happen in the process), was a superior approach to Add/Remove Programs or find package name/uninstall with package manager approach of most distros. So maybe you are a die hard fan of old ways, but it clearly is a mess and not user friendly at all. Just look at why the LSB was created and more importantly, why nobody is following it 100%. If that does not seem like a problem to you I don't know what to tell you. As for the root structure, they do mention in the article that it is optional. It can be turned off by disabling the kernel extension.