Both dramas are highly political, both have leads who dream of a fairer world and besides, Han Seok Gyu plays amazing kings in both (I never thought I could see him in another king role because I thought it would never be as good as Se Jong, but guess what he's just as good as Young Jo or even better.) Both are equal in quality of story and development of characters and both dramas deal with factions that oppose each other. I just feel that if you liked one, you will like the other.
Secret Door's King Yeong Jo and Cruel Palace - War Of Flowers' King Injo share a lot of similarities emotionally and in portrayal of characters. Both kings are portrayed very human and with lots of emotions, fears and scars and fragility. Both kings were enthroned by a coup. Also their relationships with their sons are very similar too, with very conservative fathers and less conservative sons. Also, I'd like to say Cruel Palace's Crown Princess is almost like a female version of Secret Door's Crown Prince Sado. Both dramas are very political and I feel that if you liked one you will like the other.
They both share similar plot lines. However, In six flying dragons there’s more scheming for the throne and it’s before joseon was established. I think of secret door as a continuation as it is 21kings in, so it’s more about how they can continue to help the commonners and the lower-class of society whilst dealing with opposition from the nobility. They are both great political dramas for me anyways.
Both are heavy political dramas and have a Crown Prince as ML. Both crown princes are very similar and want to be good kings who really care for people. Haechi has more action while Secret Door is more psychological. One thing to keep in mind is that the 2nd male lead in Secret Door is also the main character in Haechi. Both characters and dramas are based on true story. Obviously each drama tells its own version about personality of this prince (and later King).