[eluser]nuwanda[/eluser]
This is a no-brainer.
Since every PHP framework (Drupal, Joomla, Wordpress, etc.) is written with PHP, then raw PHP is the superset of all such frameworks.
Codeigniter is closer to raw PHP than most frameworks. That is, it uses less abstraction than the aforementioned frameworks.
It's not a question of outgrowing Codeigniter, it's a question of requiring more abstraction.
I use Codeigniter precisely because it abstracts just enough of PHP to make me happy and productive.
I can write lots of raw PHP but fall back on CI when I need to. I can even include PHP classes and functions that have not been written for CI (such as Zend classes).
If you need more abstraction, then use it, wherever it comes from.
[EDIT] I should say that I use Wordpress all the time for quick development where it suits. But sometimes, it's just too much.