Your argument has a fundamental problem: you begin by saying narrative quality is subjective and that there is no credible objective criterion for determining the greatest piece of media, but then you make claims that Shikamaru is better written than Chopper, Blackbeard is poorly written, and Code Geass handles political themes better. You can defend those comparisons, but you still need to establish consistent criteria for them instead of treating your own judgments as self-evident.
More importantly, you're assuming that a work must be the best or nearly the best in every individual aspect to be considered the greatest overall. That isn't logically necessary. Overall greatness can come from how different elements work together, rather than from winning every individual category. A story can have the best political commentary, another can have the best dialogue, and another can have the best individual character arc without any of those automatically being the greatest complete work.
Your argument about Chopper also confuses overcoming trauma with forgetting it. His backstory establishes his rejection, his relationship with Hiriluk, and his desire to become a doctor who can cure any disease. His ability to enjoy life after finding a family doesn't mean his past has become irrelevant or that he has forgotten it. It can mean that he has finally found the belonging he lacked. You can argue that his later development is inconsistent or underutilized, but you haven't demonstrated that his characterization fundamentally fails simply because he becomes happier.
And even if I concede that Shikamaru is better written than Chopper, that only proves Shikamaru wins one character comparison. It doesn't establish that Naruto is better overall. You would still need to compare the complete works across their respective strengths. The same applies to Blackbeard: a character doesn't need to undergo the same kind of emotional development as Shikamaru to be well written. Ambition, thematic significance, narrative function, and characterization are also relevant criteria.
Your Code Geass comparison has a similar issue. Yes, Code Geass develops its political conflicts at a faster pace and concentrates its political drama around Lelouch. But speed and directness aren't the same as superiority. One Piece uses its scale to explore authoritarianism, slavery, corruption, historical suppression, and freedom across different societies. Whether Code Geass handles those themes better depends on what you're evaluating: efficiency, complexity, consistency, or thematic integration.
Finally, I'm not claiming that One Piece is objectively the greatest piece of media in a way that everyone must accept. I'm arguing that your objections don't establish that it cannot reasonably be considered the greatest. If your position is that there is no universally accepted objective ranking, that doesn't invalidate the possibility of making a defensible case for one work being the greatest overall. You need to demonstrate why your chosen criteria should determine the result, rather than simply point out that another work does certain things better.