It probably makes most sense for ProtoStar to load `user.css` last but there are a few ways to work around stylesheet load order issues without hacking the core.

**1. jQuery Easy**

[jQuery Easy][2] can be used to remove the stylesheets and then add them back in the desired order.


**2. Specificity**

Make custom CSS changes specific enough so that they override the other stylesheets regardless of the stylesheet order.

Reference: http://joomla.stackexchange.com/a/15853/120

**3. Use a Third Party Extension to load your custom CSS file**

Instead of using `user.css` for your custom CSS, try some third party extensions which may load custom CSS files in a different order compared to the ProtoStar `user.css` stylesheet. For example, [EasyScript][1] loads a custom CSS file e.g. `custom.css` last.

Reference: http://joomla.stackexchange.com/q/15852/120

  [1]: https://extensions.joomla.org/extensions/extension/core-enhancements/coding-a-scripts-integration/easyscript/
  [2]: https://extensions.joomla.org/extension/jquery-easy/