I use Chocolatey quite a bit now and can definitely agree with the hack aspect of it. It's not always clear when a package will need your input (since they couldn't automate that part) but for the most part it works.

I am hoping that since package management is now an official Microsoft effort, a large gain will be to address these "hacks".

The long term potential of this is that enterprise can build their own repository and push changes out as they wish. This would be the real value. Also, companies that already provide package/software deployment solutions will now have another tool to help them do this.