Hmm, I find the story and characters in P4 to be really pedestrian. I read a lot of books and watched a lot of anime like Detective Conan, so murder mystery isn't very new to me. Furthermore, P4 in general does it pretty badly. At least to me, the fun of murder mystery comes from suspense as the protagonist reveals more clues in the midst of imminent danger. 50+ hours into the game and nothing interesting has yet to come. Part of it is that the action is so drawn out. You only really get new clues as to what's going on every time someone is kidnapped, and there is a huge time period in between where you're just doing other stuff (getting social links). Its even worse if you play like me and rescue the person on the first day that got kidnapped because most of the fun you get from the game comes from maxing out social links rather than pacing your way through dungeons. You can say p3 was exactly the same in that way, but p3 wasn't trying to be a murder mystery. In that game, social links were more strongly integrated into the story. The game didn't revolve around episodically saving individuals, it revolved around becoming strong enough to overcome a great adversity every full moon. So as for the immediate goal, p3 made sure it was always ahead of you, while p4 allowed you to achieve it and have nothing to do until the next immediate goal came up. The whole social link system also really ties in with the overarching memento mori theme of p3. In p4, it feels more like p3's system shoehorned into a murder mystery rather than an integral part of the game.
Furthermore, its not really you gathering the clues, its you watching a group of teenagers bumbling into the obvious conclusion. The game is way too slow paced to be a murder mystery, without the satisfaction of watching clever deductions.
As for characters, I felt p3 did a much better job with them. They all had problems, but p3 was a lot more subtle, rather than relying on a cheap plot device that allowed you to pretty much see their major problems all at once. Sure, you have the individual social links, but the meat of the story just gets exposed all at once for the most part as opposed to p3 where you had exposition throughout the story as well as the supplementary social links. P4 to me feels like it takes a run and gun approach where they just systematically take each character, expose his story, and move onto the next one. So for me at least, it felt like p3 was telling a better story of their characters, where since they didn't reveal all their secrets, dialogue and expressions had a lot more significance. I also just happen to like the p3 personalities a lot more for the most part. The one thing that annoyed me was how Fuuka's voice got slaughtered because trying to emulate Mamiko Noto is for the most part a failed effort, even for japanese people. (Doesn't help that Mamiko Noto is arguably my favorite va ever).
What I really liked about p3 though was how it took the common theme, "memento mori" and really ran with it. While you've seen plenty of murder mysteries before (even weird ones) you've never seen somebody metaphorically blow out their brains to summon monsters to fight for them. That single image alone I find much stronger than anything p4 has thrown at me yet.