I think it's most important to be able to attach metadata to notes; next come plugins, next - notebooks and tags are 'nice to have' and I wouldn't miss them if they weren't available.
My reasoning is: The notes are the most important, because that's the entire point. I can, for instance, say 'this note is synchronized to system X, where it has ID Y'. I need that per-note.
Per-plugin data would be great for configuration sharing and the like - connection strings, settings, etc. It can be worked around using notes - currently, I'm still using this:
Summary, so you don't need to click that link: my CLI app, plugin, or whatever, have a hard-coded GUID that refers to a note with the plugin's configuration; it stores any config there. (Or, if need be, any per-note metadata.) I just put anything in a data structure, then serialize it to JSON and store that in a specific note.
That works, because since the ID is hard-coded, there's no need to sync it between instances; and the contents themselves are synced as a standard note.
It's kinda okay when it comes to syncing plugin config; not so great for per-note metadata, because it requires having a huge note with a serialized dictionary with KVPs for each note.
Last but not least: we would need a UI to show the metadata. I think it'd be quite sufficient to have a link for 'show note metadata' in the Info section where History is, which would just show the data for the note. (A read-only table would be fine.)