[eluser]xwero[/eluser]
it are not only the things you mention that make the validation take up too much space in the controller but also the control structure, upload manipulations, callbacks, and other things. Keeping things in a config file also makes it easier to loose oversight of what you're checking because you have to mentally make the connection instead of seeing the connection with the validity check.
It's not because the CodeIgniter file is in the system directory it shouldn't be touched. It is a part of the bootstrap file and you should customize it the way you want. By changing the include of the file you can customize it per application but if you want it plain you can use the default one.
A lot of things can be done by customizing the CodeIgniter.php file where you would need to extend the controller instead, which adds another layer to your application. But customizations should span the whole application otherwise extending is a better option.
The OP speaks of forms shown on all pages so that condition is met.