Installer classes have nothing to do with this because they're called after
everything has been installed. It's too late to alter what's been installed.
The idea that you can do this seems to come from the belief that the Install
method installs everything, and you change behavior by overriding it.
However installs don't work this way.

It's almost possible by adding the custom dialog with checkboxes and using
the properties associated with the checkboxes as conditions on the files
installed, but it's a one-way trip because you can't modify anything
afterwards.

This is usually done (and here I should say "in fully functional setup
tools") by having files grouped into features that the user chooses with a
standard dialog (like installing VS 2005). If you change your mind later you
can do a modify and alter what's installed, adding or removing features, but
Visual Studio setups don't support any of this.