I hate to say it because I still think it's a good game, but Persona 3 is the most disappointing of the PS2 Megaten games.
More disappointing than Devil Summoner. Oh TVC. 
Yep. I liked Devil Summoner, although I figured Persona 3 would trump it. Devil Summoner was what it was, nothing more nothing less. Persona 3 is just blown potential. And a terrible soundtrack. I thought Persona 3 would really be open-ended, and allow you to develop your character however you wanted. Unfortunately, there's only one correct "tree" through every interaction, so only the illusion of choice is there. Coupled with disappointing dungeon crawling and the worst megaten soundtrack ever, Devil Summoner easily laps Persona 3. The only thing Persona 3 has over the other PS2 megaten games is the localization.
Devil Summoner is Megaten lite. It has a watered down fusion system, easy as shit difficulty, boring battle system that isn't deep at all, random battles in towns, so forth. Persona 3 however, has challenging boss fights, a great battle system that's an evolution over Press Turn, a good story with good characters, good localization, and interesting take on an established genre. P3 has a hell of a lot more going for it than devil summoner. The only good things about devil summoner is that it, like P3 is an experimental game so it's pretty unique (although it doesn't nearly pull its experiment off as well as P3), the story (somewhat), and localization. It's by far the weakest SMT released stateside, while P3 could be arguably be considered the best. Persona 3's October boss fight was better than all of Raidou. Truth.
Music aside, which I pretty much agree on, I disagree entirely about what you say about P3. The dungeon crawling doesn't have any puzzles to it, but the quests add variety and fun to the dungeon crawling. Plus, the guardian boss fights can be a total bitch and require a few tries. The fact I can die at any moment because I have the wrong Persona equipped makes things just as interesting. Devil Summoner didn't feel like that at all. That game is easy as shit. While it's true that when talking to npcs you have to pick the right choices to level up the S. Links, P3 isn't open ended in that vein at all. It's open ended in that you can choose whatever the hell Persona you want to level up through S. Links. Often on any given day you have the opportunity to pick 10-12 different S. Links at once. This variety makes the game interesting 60, 70 hours into the game.
Hell, Digital Devil Saga is lower than Persona 3. It doesn't even have fusion or monster collecting.