I've only got 2 minor complaints so far about 6 hours in. One being that I don't like the border around the screen in dungeons making the playing area that much smaller. I think Atlus went a little too overboard with the interface layout and it's kind of overcrowded and in the way a bit. It's not that bad, but it's a bit much covering the gameplay.
The other minor complaint, and I don't know if it holds for the future story dungeons, but the way the first story dungeon is done is that you do a section of the dungeon and then hit a cutscene and retreat, then the next time you do a different section and then hit a cutscene and retreat, etc..etc.. until you get to the final end run of the dungeon. Not a big fan of forced piece-mealing the dungeon since I just wanna dungeon crawl, so I'm hoping the future dungeons don't follow this structure, but I could see them use this structure for all the dungeons possibly to make them more story-focused.