Multiple CI on one website?

[eluser]ammtar[/eluser]
Hi,
Maybe silly question but...
My current website (ecommerce) has lot of modules (directories, profile manager, forum, event registration, membership, forms (membership renewal, event registration,...), ...)... and switching to CI would be pain in the neck and time wise impossible. What can I do is do it step by step, adding new modules using CI and when update a module (e.g. Directories) switch it to CI.
To do that it would be REALLY helpful if I can have CI installed within the each module. Something like
www/
diectories/
applications
system
prof_manager/
applications
system
events/
applications
system
reg_forms/
applications
system
etc.

Is it possible? If yes is it "smart"?

Or there is an other option?

Thanks.