To solve the problem of having hunderds of tags and scrolling up and down a long way, and may be missing what you are looking, and more importantly to make the use of tags more organised I suggest the following, hoping any of them is doable as a plugin
- tag stack.. borrowing from Evernote's Notebook's stack idea. Tags would be viewed inside containers or headlines or titles (not necessarily restructuring them), so the user can collapse the view of some of them and expand others.
- Add a search for tags in the left side panel (not for the notes having a certain tag but for the tags themselves), thus showing only the tags matching the search term.
I think this feature(s) if possible via plugins would be really useful, especially for heavy-taggers like mysled and most Evernote migrants