These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
YMMV: The Borgias
Copy Cat Sue: In-universe, Ursula to Lucrezia. With her blond hair, hairnets, the way she meets Cesare directly after his dance with Lucrezia, and abusive husband, she is basically a stand in for Lucrezia that Cesare can actually have an affair with without the incest.
Fan-Preferred Couple: Cezare and Lucrezia, so far. Historically speaking, they may have actually been a couple, as well. Season 3 episode 3 finally makes this canon.
Fetish Retardant: Juan and Sancia's chemistry exploding into sexual passion? Hot! Juan and Sancia's chemistry exploding into sexual passion against the table where Sancia's father has seated a bunch of dead, mummified bodies? OH GOD NO MAKE IT STOP.
Foe Yay: Both Cesare and Rodrigo have this for Caterina Sforza. When trying to get the Sforzas as allies in season 2, Rodrigo talks about how he wants to feel her "beauteous lips on our...papal ring" (complete with extremely suggestive pause). Cesare later repeats this line pretty much verbatim when he meets her to persuade her to come to Rome. Her conversations with him are dripping with innuendo from both parties. They screw each other passionately for a couple of nights, only for her to openly defy the Borgias in the morning.
Hollywood Homely: We're told Calvino di Pallivinci pales in comparison to his brother in looks.
Idiot Plot: After Paolo's death Lucrezia refuses to feed her baby. While everyone is looking for a solution because the child is starving no one thinks about finding a wet nurse (an issue that had been talked about in the first episode, and never again).
And yet possibly avoided with the other plot in the episode being more or less solved in the first quarter. Lucrezia knows Paolo cannot read or write, knows Cesare arranged the meeting, her mother allowed it...but that Juan attacked Pablo for even speaking to her. Rodrigo and Cesare confront Juan...who is, true to his character proud of what he did to defend the family's "honor" and confesses. But see also They Wasted a Perfectly Good Plot.
Incest Yay Shipping: The majority of Internet fans ship Cesare and Lucrezia. To be fair, so does history, which latched onto the rumor of her being in relationship with both her older brothers and her father (who is the assumed father of her known child).
Magnificent Bastard: Cesare is this in more ways than one. He's already the other kind of bastard, spends most of his free time plotting with his dad, manages to see problems patriarch Rodrigo missed from a mile away, and managed to escape the French troops in no time. Admittedly, his guards were Too Dumb to Live, but still.
The three of them each have subtley different takes on this trope. Rodrigo is at his best with one-on-one manipulation and charm. Cesare is mainly The Strategist and prefers to cleverly outwit the enemy rather than manipulate him. Lucrezia relies mainly on personal magnetism and an innocent persona that is only partly an act.
Cesare's candidates: He ordered the murder of an innocent bystander in order to save his father's political career. Building a relationship with Ursula completely around lies, then killing her husband. The ruthless torture of French soldiers, and lastly, the murder of Giovanni Sforza, though we hardly mourn for either. Finally, murdering his brother Juan may have been necessary given his increasingly dangerous behaviour, but the fact that he carries it out with no remorse or emotion apart from vengeance shows the Protagonist Journey to Villain is finally complete.
Juan's Curb-Stomp Battle with Theo, which only occurs because Juan's an idiot who believes in gossip and can't control his temper.
His murder of Paolo is perhaps a better example of this. Lucrezia certainly thinks this.
The French army crossed it when they massacred Lucca. After they agreed to surrender.
As an extension of this, despite his foolish inability to realize exactly how brutally the French would act, instigating the French invasion of his homeland can be considered Cardinal della Rovere's.
When Ludovico Sforza had his nephew poisoned right in front of Ascanio, all the while saying that he will gladly welcome French arms with open arms of his own.
The Scrappy: Ursula is pretty well despised by the fandom partly due to the lack of development in her relationship with Cesare, but mostly due to her Mary Sue qualities that make her appear flawlessly perfect.
Stuffed In The Fridge: Maria, the maid in "The Assassin". Micheletto seduces, then brutally murders her, with her death being the "proof" needed for Micheletto and Cesare to set up della Rovere to be banished from Rome. She basically dies so the audience can see how ruthless Micheletto and Cesare are, and to set up della Rovere's revenge angle.
Arguably, a male version with Paolo. His story function was to give Lucrezia the natural-born son she may have had in history and a paramour whom she loved, then die tragically. He's more or less a Purity Sue.
And now, Ursula is dead too. Since she's regarded as The Scrappy by most people, it's unlikely anyone will be too upset by this, even though Cesare all but lampshades the fact that her role was to make him more ruthless; "[her death] has released my heart of all emotions but one: vengeance".
Squick: The various torture scenes, most of the gore is actually offscreen but that's bad enough.
Gioffre's wedding night. He's a kid of thirteen (and looks younger) who's about to have sex with a grown woman, he may look happy about it but that doesn't mean the audience is.
They Wasted a Perfectly Good Plot: The murder of Paolo is more or less resolved in logical but very undramatic fashion in the first fifteen minutes of the episode following. Lucrezia remembers Paolo did not read or write and couldn't sign his name, much less leave a suicide note; she knows of only three people who even possibly knew about them and two of them, if not in favor, were at least accepting; and the third reacted violently to even the possiblity. She mentions Juan to Rodrigo, who confronts him with Cesare and their mother, and Juan admits it, because he's proud of "defending her honor".
While it's mostly for the sake of being allowed on television, cutting out the incest within the Borgia family does remove a rather important dimension of their dynamic as well. As of season 3 episode 3, Cesare and Lucrezia's Incest Subtext has now moved up to actual sex.