I've had Logos almost since it was first available and use it regularly. I like the convenience of the notes files, but the implementation remains amateurish. Could you AT LEAST make these improvements:
1. Make it so a note file can be split up into multiple files (export a portion of the tree) and allow a note file to be imported into another one.
2. Make the formatting actually work! (i.e. fonts actually change when you change them; links can be terminated, paragraph formatting really works.)
3. Allow note files to be exported into some common file format. Text file would be a good start, Word would be better.
4. Nice but not as critical: Make the indentation system to be more than just window dressing.
I know it may be a lot of work but why not make notes html files?
Just do something to show you care.