My advice is if you want to use Magento, you stay away from GitHub. If you want to contribute a bug fix to CE, then you use GitHub.
You can start a project using “composer create-project” and it will download official released packages from our Composer repo. This is how we release official patches. It will also be how you purchase extensions. What we did for the bigger ZIP on magento.com is do this for you and then ZIP the result (including all the dependencies). So its a single ZIP file to extract and it just runs.
The problem with going to GitHub is you cannot install patches via Composer. If you install a single extension from the Marketplace (live soon) you will not be able to do an upgrade later due to a half mix of GitHub (non-packaged) and Composer based installed pieces.
So, my simple advice is “never use GitHub”. When you know enough to understand the difference, then you can ignore my advice!