1. Solution I use the CTK command line interface module which helps me to publish my parameters, parse command line calls and on the host to communicate the processing parameters between my module and the application.
1. Limitation You do not have access to application features or other modules from inside your module.
1. Solution You use the command line interface support module for parsing parameter descriptions. If your application is using Qt you can optinally use the GUI generator for creating a GUI for the module parameters.