[eluser]WanWizard[/eluser]
I don't really see the dilemma, but maybe my clients are different from yours.
A CMS is about content and content management, by definition static by nature. Sometimes a CMS has some modules which allow for a bit of interaction with the user, but that's it. A CMS like Pyro is perfect, as it does these things out of the box, and as you said you can leverage your CI experience.
A business application on the other hand has little to do with content management. Yes, it will probably have functionality for users and user management, but I find that the ACL requirements for business apps often need to be a lot more granular then a CMS can provide.
If you work modular, and avoid dependencies (and you should), you need to write a custom module for that, and once written you can reuse it in every business app that follows.
If you keep to this routine, over time you'll end up with a large library of reusable modules which will give your custom app a flying start.
There are a lot of people out there that tend to use a CMS as a development framework. Joomla and Drupal being prime examples. And I think it's fundamentally wrong. If you do you'll have to carry the weight of the CMS with you, all the junk you don't need, and you are forced to work within the structure of the CMS framework.
I have a client that does everything with Drupal but making coffee. If I see the size of the teams programming, the progress they make, and the hardware needed to run the applications, I'm willing to bet that we can do it faster, cheaper, and produce better results. By using a development framework instead of a CMS framework.
The only issue I have with CI when it comes to custom app development, is that it lacks features required to build large scale applications fast. No support for modular programming, no namespaces, the singleton pattern, lots of third party stuff that is bolted on instead of integrated in the core (with all issues related to that), etc.
I've grown out of CI in that respect, and use another framework, but for CMS based apps Pyro is still my number one choice.