[eluser]iamzozo[/eluser]
Not a troll topic, but sometimes it get well discussed. But it depends on where you ask this question. Maybe on drupal.org you get different answer
I think there is not a good answer for this. Sometimes many drupal developers like to call drupal as a content management framework, not a cms, because of it's many functions which can use like codeigniter's. The main difference is the prewritten modules, in that case if you want to develop a website. I much like codeigniter over drupal, it's clean and simple. You can write what only you need, no other modules, functions, hooks involved. I created 2 websites which based on codeigniter. The first one took me 1-2 months (weekend job), but the next one was much faster, because i had the "cms" already.
Drupal is a very robust and complex system, and you can do a lot of things with it. But if you prefer codeigniter and if you have TIME i suggest go on with CI.
Write your own modules like blog, comments, categories, assets, users etc. and next time you don't have to worry about it. There are a lot of great libraries which handle things like user management and it's also flexible, like formgenlib, ionauth, imagemoo or a datamapper.
With these libraries you can create a basic site functionality in a few days.
And what i like most in this workflow and ci, that i only do what i need, nothing more.
I'm a designer not a developer, and i have worked with a few drupal site where i had to create themes for it. What i don't like, it was the hacks what i had to do in css, and to build upon the generated code, when sometimes i miss some divs or there were to many

So the exactly difference for me is to create a design for drupal or create the output code for the design (view) - in ci.
So i think the main question is always will be different, it depends on where and who you ask

Somebody suggest it, to do a site in drupal and one in ci, and after it you can decide it
To get confused a bit:
"Custom code is not evil".
"There is a module for everything"