dennis,

I was thinking of putting a piece down in place of the transition then run the other boards to that diagonal piece. So pretty much they will all be ran the same way with a diagonal piece dividing it. How would that look?

ewwwwww, lol. I would find it objectionable, but then, I don't live there. Ask yourself, since you have the deciding vote.
OR, you could lay all of the new floor in the direction the transition is now running.