It might be better not to address the balance thing at all, and let people fill in the gaps themselves!
Well, if you wanted to keep the Chosen One/balance stuff, maybe the Force has been out of balance because this malevolent spirit has been leeching off the Force for the past 1000 years, like a cancer. So destroying that entity is how balance is restored.
Instead of having a whole bunch of Force ghosts, it could just be Anakin that appears. You could superimpose brief glimpses of Anakin’s spirit onto Rey as she is deflecting the lightning, and then when she starts deflecting it back at Palpatine, that spirit becomes more solid, and finally his spirit could fly toward Palpatine, and that collision causes the explosion. So basically, its like Anakin’s spirit is dragging the Sith entity into the netherworld for good. It would be an interesting dichotomy, where you momentarily have these two avatars of the Sith and the Jedi having one final confrontation.
You are probably right though, it would probably be less work to just remove the Chosen One stuff from the prequels, and infer that balance is just a thing that has to be maintained constantly, rather than some prophesied being bringing some ultimate form of balance.
Also, when thinking about how to improve the climax of the film, I can’t help but think back to ROTJ. To me what made that climax so great was the emotion of those final moments between a conflicted father and a selfless son. Will Luke give into his anger? Will Vader save his son? Suddenly the epic battle between the Rebellion and the Empire became a very personal conflict.
A lot of the emotion that I think exists in the IX climax is the interaction between Ben and Rey, and between Rey and her friends. Rey really has no actual personal connection with Palpatine or the Force ghosts. While I think having a part of that ethereal battle between the forces of the light and the dark side is cool, I also thinking finding ways to make the final battle feel more personal would make it generally more satisfying. Does that mean replacing the Force ghost talk with something else, or pairing it with something else? What else can be done to heighten the emotion of the climax? I think that is something to think about.
EDIT: Cool thoughts Starkiller! I think having Kylo’s search be for the fleet would be a good alternate. Do you think you could transcribe Poe’s exposition about the fleet and “Somehow, Palpatine returned.” To see how if excising any mention from that scene is possible?