The View Shelf menu can be reduced in size by going to Customize plugin and unticking the Active column for all the shelves you do not want to appear on it. You can still add books to non active shelves, you just need to toggle the filter on the add to shelf screen.
Putting in a context menu action for prefixing tags for hierarchical purposes is probably a bit too much of a niche action I think. Lets see if other people ask for it. Personally I think the subset of people who have so many goodreads shelves that the paste action becomes too much is pretty small. Then you also need to cater for what if there are multiple tags mapped to that shelf - does the prefix go on all of them etc.
Not entirely sure what you mean by linking tags, but if you mean synchronising the mappings for the Goodreads metadata plugin vs the mappings in the Calibre Tags column on the Goodreads Sync plugin, then that would definitely be a no. The "shelves" that the Goodreads metadata plugin pull back are Goodreads defined shelves that are generic genres. Now while some users might have their own identically named shelves subset, many will not (like me) so it makes no sense to try to combine them, even if they weren't in completely different plugins. I can understand how in your case if you are trying to use identical personal shelf names you can see some duplication, but again I see that as an exception rather than the norm. Also the way I envisage this plugin is that users will exclusively use a choice of "Add to Shelf", "Sync" or "Upload/Download shelves as tags", whereas since you appear to be using combinations of at least the latter two you are again creating more work for yourself than other users may face. You are welcome to use the plugin any way you choose of course that makes sense to you, it is just not a use case that I see as a common one.
But then I *only* use the Add to Shelf function, which means I don't need any shelf/tag mappings beyond those setup for my Goodreads metadata plugin, and I only have a small number of shelves which are not based on genres, so my usage is entirely different to yours
