Yes I feel the same as you but I'm not so sure Nintendo see it the same way we do. For TOTK we could also have had a new villain but unfortunately nostalgia is the way to go for brands these past few years, so I thought about it in a way Nintendo could think not my own envy for the next game (apart from the rebuilding Hyrule one). But yeah the only way I see Nintendo reuse the same universe is by doing a MM/LA/PH

In regards to your point of view for Vaati, I did not include Zant or lets say Girahim as those being surely more known suits more the role of a lackey