@d2010, I am not sure if I understand. Are you suggesting to have many .todo files for a project? It may not be needed often. The most logical place for ToDo items is still inside Pascal source files, near the place where a planned code will go. A .todo file is useful for initial design phase when a project does not yet have source files for the planned features. Then those planned features can be listed in a single .todo file.
The ToDoList plugin must not take all .todo files it finds in the project directory. Remember, there can be multiple projects there. However if many .todo files were added to a project (in Project Inspector) then the plugin could read them.
If somebody wants to implement it, please go ahead. Patches are welcome.