[eluser]jjDeveloper[/eluser]
Another suggestion is using Wordpress and bootstrapping codeigniter into your Wordpress theme if you want to use codeigniter to perform tasks.
This worked for me as I saw it like this
MVC design pattern
Wordpress = controller and view
Codeigniter = model
Now you can have a custom app in codeigniter which you can use in your Wordpress themes.
It's a heavy way of doing things but you get the best of both worlds.
<a href="http://ellislab.com/forums/viewthread/209516/">CodeIgniter App integration with Wordpress</a>