CakePHP leverages the default layout where implementing the header, footer or sidebar is easier. While CodeIgniter create the view or layout with the direct approach, which appears like the app was built from the ground up. Plus, CodeIgniter also provides a caching mechanism for the view that makes the work easier.
If you prefer the MVC pattern then you'd naturally favor the CakePHP over CodeIgniter. However, if you are new to frameworks, you might prefer CodeIgniter since it is a lot simpler and easier to learn.
