I hope version 2 could go further and not only be a clone of evernote --- nixnote can be nixnote itself ! We don't need to limit ourself within evernote's format.
A possible way could be considered : sync filter. That is, nixnote can internally use its own file format. When need to synchronize with server(s), we can "filter" the data to adapt to different server format. For example, if we want to synchronize with evernote server, we can filter those xml tags not supportted by evernote server. A simple way is escaping these unsupported parts with "magic escape sequence". When displaying with evernote client, these parts are just "random characters", so nothing is lost. On the other hand, we could synchronize with nixever client and get the original version. We could even further synchronize with other third-party server, as long as we write its sync filter.