Cover stories always fall into 2 categories:
1. They either, very plainly, update us about specific locations or characters
2. They do the above whilst driving forward a particularly major plot to a future arc.
We can go through each and I'll label them a 1 or 2, but earlier cover stories usually didn't lead to an arc, but rather maintained a characters relevancy in the manga.
- Buggy (1): Kept Buggy relevant until Loguetown and shows how he met Alvida. Does not lead to a specific arc.
- Koby/Helmeppo (1): Shows how both became friends, worked under Garp, and became much strongeram as Marines. Does not lead to a specific arc. They were last seen post-Reverie.
- Jango (1): Shows how he met Fullbody, Hina and became a Marine. They were last seen at the Reverie.
- Hatchan (2): Showed how he escaped the Marines and how he met Caimie/Pappag. Technically, it led to Sabaody, so it falls into the second category.
- Wapol (1): Shows how he became a King for a new country in a comical way. Became relevant again at the Reverie.
- Ace (2): Tied to his search for Blackbeard. Led to an entire 100 chapter war plotline about him and Whitebeard.
- Gedatsu (1): Showed the happenings of Gedatsu. Tbh, while this probably the least relevant cover story in the series, it mainly showed how Alabasta prospered and how Vivi was doing. Both Vivi and Alabasta are major plot points post-Reverie, to which we are anticipating what happened.
- Ms. Goldenweek (2): Myriad of character updates but most importantly is it led to Luffys encounter with most of Boroque Works at Impel Down.
- Enel (2): I'm putting this at a 2 for now. Its by far the oldest cover story that has yet to pay off, outside of the 2 most recent ones. There is clearly a ton of mysterious air about the moon stuff and what it means. It still is a mystery, and we are awaiting Enels return because of it.
- CP-9 (1 OR 2): Right now its a 1. It led to Lucci, Kaku and Spandam returning as CP-0 members. However, we have no idea how it came to be and we have no idea what it really means. Is Lucci still evil after being saved by the doctors? Are they infiltrating CP-0? Whats going in here.
- Strawhat Separation (2): Obvious why its a 2 and what it leads to.
- From the Decks of the World (1): Finally gave us a full update on most One Piece characters and locations from the series, but it mostly was fanservice outside of maybe Vivi's updates again
- Caribou (2): Led to his misadventures with Jinbe and eventually falling into the hands of Drake. This led to Wano's story.
- Jinbe (2): Purely led him to WCI, obviously enough.
- From the Decks of the World 500 million bounty (1): Like the first one, same deal.
- Strawhat Fleet (2): 100% leading to something eventually with the characters, we know this already from the plot.
- Bege (2): This one is a prediction but I think his is definitely leading to Elbaf, as is Enel's. One is tied to finishing BMs story, while the other is about answering more about the World/Moon/Sky and so forth. The Giants will definitely reveal some things about the world and the "Giant Red Serpent" is probably Jorgumandr or Red Line. Their huge tree, Yggdrassil might be an avenue to explore all of this.
Because of the way the above has gone I am placing my bets on Caesar being the next one. He want entirely MIA last arc and I dont believe Vegapunk is next, but Elbaf is or a prelude island to it. Caesar and potentially Germa will lead to Vegapunk in the end.
It is also possible Vegapunk's facility is at Elbaf, just hidden, considering his studies with Giants and the like. Elbaf could just be a massive amalgamation of pre-Final War storyline that he needs to finish:
- Loki and Lola/Big Mom
- Vegapunk and the SSG
- Enel and the Moon
- Urouge and his motives
- Bonney and Kuma
- Sabo and his commanders
- Rocks stuff
- Underworld stuff
- Impel Down silver medalist stuff (which i think is Rocks stuff)
- Shanks and Blackbeard
Etc. If Oda isn't willing to split up these plotlines