[andrewjshults]

The biggest problem I have with CI as a specific application framework is the insistance of being extremely backwards compatible (PHP 4 support was dropped less than a year ago, and they only very recently stopped supporting 5.1). I understand why this makes sense for Ellis Labs (the developers of it) since Expression Engine is designed to be deployed by clients. If you're picking a framework to use, pick one that allows you to take advantage of all the improvements made to the language (PHP 5.3/5.4 bring a huge number of improvements over even 5.2). I also have a number of fundamental disagreements with how CI is built - no proper autoloading system, a weak routing system (no URL helper/parameter mapping), no request/response objects, odd controller instation and library/model loading (generally fairly disconnected from standard OO design)

If you want a full featured framework, Symfony2 is a good everything including the kitchen sink although it's a bit more Java-esque (which make sense since much of PHP's OO design is based on Java). http://symfony.com/

For something lighter weight, Silex is based on the Symfony2 components, so it's super easy to pull in more components as you need them. http://silex.sensiolabs.org/

Even if you're not using Symfony2 it's really modular and easy to integrate with other frameworks - we're running CI as our base framework due to legacy reasons, but all of our new work leans heavily on Symfony2 components.