I don't expect any of these to actually be implemented by Microsoft as they are all major design changes, but, to name a couple:

Central standard system for software configuration.

This would be similar to the Windows registry but with larger scope. Every setting of any software would be configurable here by users. No nonstandard config files. No trying to find config files everywhere, etc. The Windows registry is only used by some programs, and in my opinion, is not at all user friendly.

This would apply to the control panel and internal settings as well. The current control panel has many different inconsistent styles for dialogs and configuration screens and can be tough to learn and tough to know where to find some things intuitively (eg: to restart your network you have to go through a 'network adapters' page).

Package Management

Windows has made strides with Windows Update, Add and Remove Programs, and standard installers, but there is a long way it could go to entirely streamlining this.