It wasn't so much a manuscript that was found - it was a heavily annotated copy of Chapterhouse Dune. It apparently held so much information that they've decided to produce to books as a sequel to the events of Chapterhouse.
As to why they did not work on these right away - who can say?
The story goes that Dune fans requested prequels but I suspect the reason was probably somewhat more contractual than that - if you get my drift.
I'm hoping that the results of the sequels will be better than the prequels but only time will tell.
