We are currently fixing an issue that causes 2.0.x upgrades to fail when they are installed with a .zip archive and then updated with either a composer-update or the System Upgrade tool. We will update this post with a resolution as soon as possible.
Any news on this topic?
Update coming soon @SKeutmeier, sorry for the delay!
New releases resolve issues encountered by some users when upgrading Magento 2.0.0 and 2.0.1 products. The issues occur with products that were installed from a compressed archive (.tar.gz, .zip, and .bz2); merchants who used other installation options are not affected. Please note that there are no issues with the core Magento application or the security enhancements. More information is available in the Magento Forum announcement and the detailed Technical Bulletin.