Well if I gave you a true in depth answer to how I would change Bonnie’s storyline it would have to be published as my first novel and you would need about 8 hours to read through all the alterations dating back through S1, so let me just give you a very general answer:
If I were to have written TVD, I wouldn’t have made Bonnie’s character, a POC (specifically black) woman the witch who consistently is used to save the day over and over again for everyone else’s benefit BUT her own. She, along with all the other witches (Bennett’s or non) are almost ALL POC, and always seem to be around just to help white vampires/supernatural beings (Lucy/Emily anyone?). Bonnie constantly sacrifices her happiness, her desires and very often even her own life just to help those around her and gets literally nothing out of the deal. This happens time and time again.
As far as Bonkai, I would rewrite things beginning with after the merge. Kai’s redemption arc would have been Bonnie/Kai’s redemption arc and I would have kept him around until she eventually forgave him. Or, even if she did end up sending him back to a prison world, I wouldn’t have had him come back as a (once again) sociopathic mass murderer (because that has zero continuity. Why give him a soul/conscious if you are going to take it away just a few episodes later? If he truly was remorseful about what happened, being sent back to 1904 would have been understandable to Kai, and he would have continuously tried to prove himself to Bonnie, even after the fact. He could have easily become an “anti hero” or sorts, by helping them fight against the heretics/keep them from coming back, rather than being the reason they cross back into reality). They really could have gone anywhere. If you can get away with making Damon Salvatore the hero who wins the love of the female protagonist over his much more deserving and tortured brother and then also play it so that everyone on the show somehow spontaneously changes courses and decides that said terrible brother deserves happiness over said heroic brother, then Kai most god damn definitely could have been redeemed. Easy. Peezy. Lemon. Squeezey.
The prison world storyline and the events that followed should’ve been a catalyst for Bonnie removing herself from the MFG once and for all.
Here’s a brief list of the selfishness, neglect, inconsideration, chores Bonnie had to deal with in just season 6 alone.
1) Damon and Elena turned their “rescue Bonnie Mission” into a date.
2) Stefan and Caroline turned their humanity off, and pursued petty endeavors instead of helping to save the woman who is the reason they’re alive.
3) Bonnie came home and was expected and harassed by Damon to participate in a mission to rescue Steroline from their irresponsible decision to turn their humanity off.
4) Bonnie’s “former lover” Jeremy didn’t stick around to see if Bonnie made it home safe.
The above are just a few instances that should’ve been incorporated into an arc that pushed Bonnie to deserting Mystic Falls.
If I were to have a say in Bonnie’s story for season 6, the following would’ve happened.
1) Bonnie reuniting with her magic and then absorbing Qetsiyahs magic, would’ve been a bigger deal. The show seemed to brush this aside though.
2) Jeremy would’ve came back to say goodbye to Bonnie, and tell her he saw her almost die. Which would lead Bonnie to asking how he knows that, which would lead to Jeremy revealing what Kai did.
3) Lily Salvatore and hereflops would’ve never existed. And instead some other magic force would’ve been locked in 1903 posing a threat.
4) Kai being the new Gemini Leader would’ve figured this threat out. And basically risk his life to save Bonnie again.
5) Jo and Kai would’ve continued the direction they seemed to be going in 6×15.
6) Speaking of Jo, she and Bonnie would’ve got closer, bonded talking about grams. Etc
7) The season wouldve ended with Kai and Bonnie teaming up to eliminate the threat. And Bonnie saying goodbye to Virginia.
Then Bonkai would’ve got their own spin off.
POC of TVD 