Hmm, I'm not so sure I appreciate the Chocolately support. I've found the packages really spotty as to where they are going to install, what options they are going to use, whether they bother to provide an uninstaller. I think a large part of that is how Windows manages installation and libraries though. In an ideal world maybe everything would provide MSIs, but they alone are not a silver bullet.
I hope Microsoft take the Updates side seriously - having many separate auto-updaters on the system all taking different views on when they should run is a nightmare. If they created an integrated third-party application update system I would love them for it.
But those are installer problems, not Chocolatey problems. Anyone who starts on the road to automated installations on Windows realises that it's basically the Wild West. Especially if you need to install XP or Vista era software.