I can't get behind the P3 train at all. Probably everyone who likes it better, or its story better, thinks that way only because they played it first, a good 10 years or so before P5. That game aged horribly, the gameplay is extremely repetitive and boring throughout the whole game, the soundtrack is good but has a couple of overused songs that get old very fast and then you have to endure them for the whole game. The game is grindy to an unhealthy degree, and yeah, the story is good, but nowhere near as good as P5 imo - it kinda feels like a prototype of a Persona story given what came next for the series. Thematically, it's really basic, and there's nothing wrong with that, but it's just not as exciting. Many of the cutscenes are awkwardly executed, too, which didn't help. And don't get me started on the multiple "time to hit on girls" segments scattered across the game.
I liked Persona 3 quite a bit, by the way. The final boss was awesome. But comparing it to Persona 5 is like comparing The Avengers to Guardians of the Galaxy Vol. 2.