Interesting thoughts. I think the back and forth (Cesare wavers, Lucrezia pushes it, then she's angsty over Alfonso and drawing away from Cesare) was my least favourite part. Because yes, chemistry like woah, they were sold as the OTP, soulmates, only a Borgia can love a Borgia...just go for it.
Also I felt there was some Ursula 2.0 going on with Lucrezia when she pushed for Cesare to love her and then withdrew, and given I hated Ursula that never sat well with me.
Jordan's boredom with the show and his insistence on trying to make us root against the characters and this relationship that he'd spent all that time making us root *for* has never impressed me and the least said about the bad fanfic that is the Apocalypse the better ;)
I think your concise summary is spot on.