For my own version to make it better:

After the queen collapse, So Yong and Bong Hwan can actually communicate with one another inside So Yong's body, so that they can at least separate their identity to make it not become like a BL story. Bong Hwan can help the king to win and So Yong will take care of the romance by overpowering Bong Hwan. It can still become funny when Bong Hwan against the romance but So Yong insist it by making it looks like a monologue, when in fact its 2 souls arguing. This drama only shows from Bong Hwan's perspective, so I thought it can be better if they can show So Yong's perspective as well. 

*If you watch the secret episode, the king and So Yong actually like one another, but because the king thought So Yong is enemy, so he avoid that feeling. 

But because of Bong Hwan's behavior inside the queen's body, the king eventually fall for her and figure out that she's not the enemy. Then, it will be like Bong Hwan helping So Yong to make king opens his heart, but don't make Bong Hwan fall for the king as well. Bong Hwan and king relationship can be just friend because Bong Hwan is originally a playboy and it cannot suddenly change him. 

Bong Hwan also can have better ending because his 'friend' the king and queen So Yong have a happy ending, rather than thinking about the king that makes it seems like he actually likes him. So Yong also can tells the king about Bong Hwan the same as Bong Hwan tells the king about modern days and its up to the king to finally believe it or not. I just want Bong Hwan to at least be known to the king because after all, Bong Hwan is the main character, but the queen gets all the credit (from the ending shown to us). 

I have two rewrites. The first deals with how I would have approached the drama in the first place...the second is a "second season" fix. I think the writers intended BH to be SY's reincarnation, so I'll keep that as I'm not against the idea of them being soul mates as part of the reason BH is so drawn to CJ, despite his identity confusion. I just hated how people refused to acknowledge the So Bong character development and attributed everything  on SY as if SB was just a puppet. 

 1. Bong Hwan would have died from his injury and So Yong died from her suicide. This mirrors the novel. I'd also eliminate the idea that the timelines are parallel and linked. BH's death prevents the audience from having to revisit modern Korea, so instead of the actions creating a butterfly effect, my ending would instead create a multi-verse where the audience is left to wonder at all the changes they could affect: CJ surviving, their child surviving, prevent Japanese occupation, prevent Korea from splitting in two, and no need to preserve the memory of King Gojong and Queen Min so as not to RickRoll'D off traditionalists...because it's no longer our world. King and Queen and child(ren) living happily with a final shot being an optimistic speech-over of SoBong talking of the possibilities of making the world a better place with CJ by her side.

 2. Second season option. BH has tried returning to his previous life. Opening scene is him in bed and we see a woman's arm draped across his chest. However, his dreams are filled with images of him as So Bong and Cheoljong passionately kissing. He wakes with a start, removes the hand of this unknown woman, goes into the bathroom and just stares at himself in the mirror until tears form. He is shown to be in therapy, trying to come to terms with his loss and the changes in his life. Under hypnotherapy, he "sees" himself and Cheoljong but in scenes not shown in the drama. Things are not miserable for them, but CJ is puzzled as to why his queen is different. While others remark that it is an improvement, and she is now acting in a proper manner and not wildly running around the palace, he can't help but repeat the phrase "yes, the perfect queen" and look a bit sad as he does so. Cut to a scene where the queen is looking in the mirror as if trying to find something in herself and BH is standing behind her. She speaks to his reflection in the glass and ponders if she made the right choice in coming back or if he really is a just a better version of her and if his love stronger.  BH wakes from hypnosis with a gasp and realizes he and So Yong are the same soul.  He finds a measure of peace in this and vows to move forward. Then the scene changes back to Joseon and we see Kim Jwa Geun. He is trying to regain power. I won't do a scene by scene here as it would be too long. Basically, KJG has someone break into the king's palace to unearth how he was able to take control (he doesn't believe CJ had it in him to do it without help - possibly from China or some other entity of power). His spies bring back the strange writings of the queen explaining military theories and the future. Something in them shows a way that KJG can stage a coup. As the coup and all that followed was a result of BH's presence in the past, the future subtly changes again, except this time for the worst. BH is confused and looks at historical information online and learns Queen Cheorin dies and CJ is assassinated shortly afterwards...not even a year after he left. He gets in his car and frantically makes his way back to the shrink so he can be hypnotized and find answers. On the way there, he experiences severe pain, loses control of his car, and crashes it into a pond...drowning. 

BH then wakes up in SY's body - in labor. The queen survived an assassination attempt but died in childbirth brought on early by an explosion. BH arrives and reanimates in SB right before the doctor is about to cut open SY's belly to try and save the baby and she successfully gives birth (some comedy here - with lots of threats directed at CJ's manly bits). The king recognizes the SB personality and is ecstatic "his" queen is alive. In my version, they work together to root out who is targeting them and, of course, succeed. This time KJG is dealt with permanently. Lots of hilarity in being a new mom and emotional scenes with the rest of the cast. CJ trying to block SB from bringing in even more concubines. A scene in which they are entertaining foreign dignitaries, and CJ panics for a moment when he sees Mr. Queen acting proper again only to relax into a smile once she breaks character...she was just doing it to make a good impression...and tells her he doesn't want a perfect queen, just her. In the process, the king believes SB's story of his soul being that of a man. In a quiet moment has asks about the future and she starts telling him about airplanes, but he says "no, I want to know about you..." She stares at him for a moment, unbelieving. They talk through the night but the words aren't heard by the audience...just a fade away of the two of them at their little table with candles burning as SB tells him of his life as BH. Later, the candles are almost nubs. SB looks at the king expectantly. The king accepts Mr. Queen's story and it doesn't matter; he loves her. She's nervous and tries to "soften" the revelation by bringing up SY and explain that she's also a part of him but the king interrupts. Tells SB that all he sees when he looks at her is "my queen." 

Next to the last scene is CJ off in the distance inspecting a new form of science that SB has introduced him to. SB is at the palace steps looking at the king  excitedly discussing the design with a couple of scholars and Prince YP approaches. He stands next to her and looks out at the king as well. He speaks to her without looking at her and says her that he doesn't understand everything and probably never will but that CJ never stopped missing her and that his smile only became genuine upon her return - implied that he realizes she isn't the same as the queen (because in my version not all of these people are idiots). He finally turns to address her directly and cautions that he doesn't want his brother, with all that he has sacrificed, to ever feel that sadness again. SB looks out at CJ and tells YP that he doesn't have to worry - she's not going anywhere. She descends the stairs and walks towards CJ and when she reaches him, her voiceover talks of the sweeping changes they will make. The new world they will create. HY brings their baby out and the voiceover continues narrating that unlike what the history books say, she and CJ will defy Fate and carve their own destiny with each other by their sides. The King asks the SB why she has such a secretive smile...is she planning to surprise him again...she replies "every day in this lifetime and the next, so you better steel yourself (a Korean version of the saying though)." He laughs happily and kisses her. The End. Whew! That was cathartic. 

 

There's a lot more (I swear...all I've done lately is just daydream about this couple and the possibilities) and some hilarity with the foreign dignitaries, one of whom crushes on Mr. Queen, but this is already pretty long, so I'll stop here. I never have time to actually sit down fanfiction - to be honest, I don't know if I'd really be any good at it - so I guess this is as close as I'll get.