I'm not saying 1-6 fit together well, or are internally consistent. I'm on the team that hates the prequels! I personally keep 1-3 in a separate place away from 4-6. When 4-6 have changes inserted into them to make them more "consistent" with the prequels (such as Hayden's insertion into RoTJ), I agree with you that 4-6 are being made into Frankenstein creations. So I like your analogy.
However, by purposeful design, 1-6 is not structurally two trilogies. Structurally, you can either consider 4-6 a "trilogy" by ignoring the prequels (which is what I do, and probably what you do as well), or consider the whole thing to be a hexalogy by including the prequels. But two complete trilogies they are not.
Episodes 1-3 are referred to as a "trilogy" for conversational convenience. A true trilogy has a beginning, middle, and end. Episodes 1-3 have a beginning, middle, and middle. Without 4-6, 1-3 would be a fragment. That wouldn't be true if it were a real "trilogy." And this isn't by accident; it's because George Lucas chose to make them that way. He chose to make 1-3 in such a way that they change 4-6 from a trilogy into a 6-parter. He didn't have to go that route (and I tend to think it wasn't the best route). Episodes 1-3 could have had their own story distinct from 4-6, which ends up resolved at the end of 3 (in the same way that 6 ends resolved) but which included Anakin, Padme, the Emperor/Empire, Luke, Leia, etc. as elements of the larger separate story.
An example of this approach is The Hobbit, which has all the necessary story elements to set up The Lord of the Rings (Bilbo encountering Gollum and acquiring the ring for example) but tells its own separate story that gets fully resolved at the end. In this way, "The Hobbit" justifies having its own separate existence alongside Lord of the Rings. The story of the Star Wars prequels is information we mostly already had from watching 4-6, without offering additional story information of enough value to justify making another three movies instead of just letting us imagine it (which was better).
However I do hope my whole post doesn't get dismissed because of a hangup on the definition of a "trilogy."