the most obvious difference between these two methods is seen here: Why is Git always asking for my password?
In fact, when I am working on Ubuntu for the git repository from oschina, I am often asked to provide the username and the passswd.
On github's page, it reads:
If Git prompts you for a username and password every time you try to interact with GitHub, you're probably using the HTTPS clone URL for your repository.
Using an HTTPS remote URL has some advantages: it's easier to set up than SSH, and usually works through strict firewalls and proxies. However, it also prompts you to enter your GitHub credentials every time you pull or push a repository.
You can configure Git to store your password for you. If you'd like to set that up, read all about setting up password caching.