It seems vim-notes is much more developed for taking general, self-encompassing notes, similar in style to Evernote. I don't see a way to inter-link the notes like vim's help, but it does have far more rich and powerful note-taking features.

I'd still use vim-wiki because it's intended to be a lightweight knowledge database similar to a mind-map, but more robust. It allows for quick, easy organization of ideas whereas vim-notes appears to be more for a formal writing process.