Even as someꦛone who is still fond of Persona 3 (it was one of my favorite JRPGs in my mid-teens), I completely agree with you

I like much more the storyline and themes of P3 than, for example, P5, but it has some issues that don't make it worthy of a 1st place IMꦆO.

𓂃The human antagonists of the story are honestly bland and not fleshed out enough even in P3 Reload. Like you point out, most of what happens in the game until the final act is pretty average/forgettable and there are even some plot holes here and there (such as the way how the mother of certain character died, which is wildly contradicted in his flashback from P3 FES: The Answer). While not as thematically strong, I think P4 mantains a more interesting and resonating story across all its acts.