Alex:
I think virtually everyone was probably surprised by just how awesome Francois & Holly's chemistry was
maybe including Jordan himself...I have already explained in one of my previous replies about why I think Francois & Holly's amazing chemistry and performances might have exceeded Jordan's prior expectations for Cesare & Lucrezia. They became so popular with fans that they just had to make the show more about Cesare & Lu by S3
Even though Jordan wanted to take inspiration from 'The Godfather', but even in the Godfather, the story was later on mainly focused on Vito's son Michael, and Cesare was Rodrigo's heir, so it only makes sense that the main focus of the story would eventually shift to Cesare in S3, and not just because Cesare became the most popular character on the show. And yes, there's been talks about how Lu had mourned Cesare's death for a long time in reality, and that's how it was depicted in every other adaptation about the Borgia family. In every other show I have watched and novels that I have read about the Borgia family, Lu was always depicted as having a very close and loving relationship with Cesare and was so devastated after he died. So for her to poison Cesare and murder their father in Jordan's book was just atrocious writing on Jordan's part
It definitely has crossed my mind before that Jordan had wrote the book just to upset the fans, I've mentioned many times before that I think Jordan might've became bitter and spiteful by the end of the series, so the book could've been his way of getting back at the fans and everyone else who had forced his hand or influenced him into making decisions & choices he probably didn't want to while working on the series. Or as you said, the book could've been used as a red herring to purposely mislead the fans and viewers, and that he had written a different screenplay for the proposed movie, I hadn't thought of that before, but I suppose that also could be a possibility. I think either way, even if they had made a S4 or that proposed movie, the screenplay that he wrote in his book would've most likely been scrapped anyway, some of the plotlines would've been kept, such as Rodrigo's death and possibly Cesare's too, I think they definitely would have Rodrigo killed by the end, no doubt about that (not sure about Cesare's death though) and have Giuliano della Rovere become the new pope. But some of the other plotlines he wrote, such as having Lu poison both Rodrigo and Cesare would've most likely been changed, I don't think Showtime or the actors would've agreed to that.