I came up with an idea that I might like for moving forward regarding this type of change. I'd add a field to the node table for 'format' and a corresponding user setting.
All existing nodes would be tagged 'e2'. New users would start at 'pc' (which would be like simplified POD: preserve blank lines and treat paragraphs containing indented lines like code). When you compose a node, it'd default to your selected input format but you could select another.
But trying to support too many input formats would probably be a mistake, so new formats should probably be added slowly and deliberately.
Just the start of an idea...