Flowey as Black Zetsu
Idea: Flowey as Black Zetsu.
They are more similar than you might think at first glance. They are both plant things(?), have the ability to travel and just pop up out of the ground, and are looking for several non-physical/tangible beings to grant them power/revive someone. In Zetsu's case that is to revive his mother, while Flowey is also looking for a revival, just of his previous form, not a separate person.
Flowey is looking for human souls, Zetsu is looking for tailed beasts. Both are non-physical sentient beings. In this fic idea Flowey would be looking for tailed beasts to combine in a single body to revive his previous form as Asriel. In this sense he replaces both Zetsu and Kaguya in the story. Flowey could become Flowey in this story in a few ways, but one way is that right before (or right after) his previous form gets sealed/destroyed he would somehow transfer his consciousness into a Flower (Possibly through determination) in a desperate attempt to not be fully destroyed.
Flowey does have a very different personality to Zetsu, he's far more playful, but that makes the idea more interesting in my opinion.
You could either keep, or not keep his ability to reset, save, and load. If you keep he could use it similarly to how he uses it in Undertale Yellow, providing save points for Madara. Or he could just use it for himself to better manipulate Madara. Another way you could use it is to have Flowey have a very different determination ability instead of save, reset and load, that being that he is able to revive himself in a nearby flower whenever he dies, keeping continuity with my earlier suggestion. (or you could give him some other completely different determination ability) There are many other things you could do of course, those were just some suggestions.
Another thing that I think that Flowey would be able to pull off is being a double agent. He is good enough of an actor to pretend to spy on the Akatsuki for Konoha or others and feed them false information, or try to get them to do things that would help the Akatsuki.
Anyway, I hope you enjoyed my rambling of ideas. (I also hope they were at least somewhat coherent)