As for whether or not we're supposed to root for them, I don't believe this is the type of show that wants the audience to root for anyone (exept perhaps Hundred Eyes.) It's just trying to show how people lived back then and in that sense I think it's doing its job.
Yes, I am looking at it in a modern point of view but this is martial arts filled fictionalised history and not a documentary. ( In real history Kaidu and Kokachin outlived kublai khan). As a piece of entertainment I think it needs a well written likable charcater to either root for or understand how the person turned bad. Take Godfather for example - Michael Corleone starts out good and likable who slowly morphs into a monster due to events, his actions and consequences.
Another example is Titus Pullo from series Rome(another historical fiction). Nearly every character on that show is unlikable when viewed through filters of present day morality , but he stands out an an affable giant but with pirate like morals and essentially the one character we root for.
My point is, we see Kublai killing a child, abusing his wife, abusing his concubines , sentencing people to death on flimsy evidence, stealing the throne, blinding a monk & holding him hostage,not making any smart descions on his own, mostly grumpy and being hideously obese. He gets the most screen time ( probably because the actor is really good & he deserves it no doubt) and the so the writers could spend time trying to make all the loyality he receives( from Polo, eyes and his sons) a bit more believable. Because at this point he is just a Mongolian Psycho.
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