Oda is less involved in the anime and even less involved in filler/movies. Anime has gone off the rails many times.
I think he lets put things into the anime that he did not think of while writing the manga or which he lets add to the anime simply because, if he were to put it into the manga it would add too much volume.
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You say this and yet, Bonney has the most panel time in this arc except for luffy, more than any of the Vegapunks. And not by a small amount either.
Is Vegapunk a critical part of this arc? Yes
But the core is clearly Bonney and her relationship with Kuma and their relationship to Nika.
edit: Also Lucci explicitly says two Vegapunks are dead, which includes Shaka and there is no indication that Chopper treated Shaka nor that Lucci is lying about who is dead.
I do not count Bonney and Lucci's panel-time. Both seem to have gotten much of it. If one has gotten a little more or less, I do not care. Both their actions can be described as having a major influence in the current arc.
Only because Bonney's problem is revealed first, does not mean that there is not another problem `hiding´ in that time skip. Chopper's group decided to head down into the basement. And even if Shaka was already dead then, Chopper would have at least looked, if he could have done something for him, if he were to come down there with a man lying on the ground, bleeding profusely. He would have needed to take off that helmet of Shaka to be able to look upon the injury. Oda skipping out on that tells me that he didn't want us to see his face, yet.
Look at how Oda tells us that 2 Vegapunk are `killed´ in that roundabout way of his: Luffy first wanted to tell the WG over the Den Den Mushi how many friends he had with him, only for Robin to interfere. That alone is strange. And we know how honest Luffy is. Meaning: He would have told the WG the true number of allys currently in the Labo-phase with him - he knows
exactly how many are still alive. It was Lilith, who cried over Edison and informed us who was supposedly dead: Shaka and Pythagoras. She even made a mistake in adding Edison to the list, hinting that she did get confused with who was supposed to be dead. This roundabout way of telling us, who is dead makes me not believing that Oda has actually killed at least one of them, if not both.
And Lucci even conveying those fabricated numbers to the WG is also a hint that he is not on the WG's side. It makes it even more questionable, if we add the fact that he was with Luffy just before the time skip and also knows
exactly how many persons are up there with him, as I do not think they would have split up after defeating S-Bear. He conveyed fake-news about the situation, got rid of Stussy in the process and now that he fights Zoro (without Zoro knowing of his true allegiance or not), he has that one joker on his side - because everyone of the WG thinks that he is on their side, even if he is not.
And the hint supproting that is that it is strange that Oda goes through all that hassle and make Kaku and Lucci join forces with Luffy with the whole One Piece fandom `flippping out´ - if I may use that phrase here as an exxaggeration - only to let Lucci betray the SHP again for Zoro to have a fight, Oda is not even focussing on? It's as if Oda is stalling Zoro and Lucci with it rather than he is concentrating on the progression of said fight.
We definitely need to see what happened during the small time skip. This is why I say that the arc is not finished, yet and we have barely scratched the surface. 😉