The story doesn't have to be totally linear for the six films to work as one. At the end of the day, it's still about Anakin and Luke, father and son, with more emphasis on Anakin, despite the fact Luke is the main character of the Original Trilogy.
Of course, seeing the films backwards gives greater context to the Original Trilogy when you get to it, but it is greatly implied that the twins are now the focus (or are going to be the focus since all the plans at the end revolve around them) of the storyline once Episode III ends. As a matter fact, once Anakin turns to the Darkside in Episode III, it shifts totally to Obi-Wan, Yoda, and Bail Organa. Anakin is a bystander by then.
We are left with Yoda, Obi-Wan, the droids, and most specifically the twins.
And whether it was originally written that way or Lucas rethought the entire Saga, you can still watch it numerically and it makes for a very compelling story about the Skywalker family.
It may work a bit better in the way they were released but it works the other way as well.