At a simple level, you could use icons to label ideas, questions, pros and cons. This would let you use filtering to review items by type. You could also use task info to keep track of answered questions.
However, there might be problems in restricting the diagram to a tree, if there are multiple links between the items (e.g. the same question impacts several ideas). This would limit the value of using a tree. A workaround would be to use floating topics to draw a network, but similarly, you would not be getting a lot of value from MindManager in this application.