First Installment Wins: And how. Nobody seems to remember there is a second part for Rudolf's adventures, called as his enemy, Rupert of Hentzau. The Downer Ending in which both Rudolfs die may have much to do with its fall into oblivion.
Rudolf and Rupert, arguably. The sequel features a scene where our hero "gripped Rupert's wrists, and with his greater strength he bent back the count's pliant body till trunk and head lay flat on the table. Neither man spoke; their eyes met; each heard the other's breathing and felt the vapor of it on his face."
Grey and Grey Morality: That Black Michael's motivations and actions are less than pure is given, but King Rudolf is a drunk and a bully who is only loved by the nobility and army, whereas Michael is the people's champion and would probably make a far better king.
The sequel, Rupert of Hentzau takes this further. Rupert is a villain and blackmailer but looking to regain his title and lands while the heroes are very ruthless in their schemes and from a certain point of view are the ones toying with treason.
When Rassendyll first meets Flavia during the coronation, and does the customary kiss on the cheek, their eyes meet. So taken by her beauty, Rassendyll smiles. Flavia is so stunned (having been used to 'Rudolph' as a bit of an ass) that she smiles back.
Rudolph thanking Rassendyll for everything he has done. It's implied that his experiences gave him a good Break the Haughty and he might be a better king as a result.
Narm: Nothing, alas! being perfect, Rassendyll's disposal of Bersonin by stabbing him under his arm, and the subsequent convenient exit of the defeated down "Jacob's Ladder" with a "Whaaaaa!" is not effective.
Jerkass Woobie: Rudolph gets locked in a prison with barely any food and water, and is nearly drowned. True he was a pompous womanising drunk beforehand, but it's implied he got Break the Haughty as a result of it.
There is something oddly sad about Flavia's little speech when Rassendyll announces he's going boar hunting (just as a way to catch Michael) out. She had assumed they would be going riding together. The way she says "I'm sorry we're not able to amuse you enough here" is said stoically but you can tell how hurt she is. Thankfully Rassendyll lets her in on the plan immediately.
To say nothing of the final goodbye between him and Flavia. He begs her to come with him, but she says she can't desert her duties to her country - no matter how much it breaks her heart to do so.
One reason Rassendyl comes off as a bit of an ass in the novel is his casual sexism, entirely ordinary at the time.
Additionally, modern readers or viewers are much less likely to sympathize with the notion that Rudolf is simply the "rightful" king, and be more suspicious of the way that Michael's supporters (which are numerous enough to be mentioned) are described as the "largely criminal" class.
What an Idiot: Antoinette seems to be the queen of ill-considered actions in this film..
The Woobie: Flavia has been one for most of her life. Betrothed to Rudolph, she had long nursed a crush for him but he constantly treated her horribly. She recalls inviting him to a birthday party and getting excited for it, but him never turning up.