Here's what I feel is the biggest "wrong" about the entire game...
I would also add something like "fusing isn't clear to people who haven't been following the series" to that list. Parts of the game felt almost impenetrable at first, and even after seeing well over 100 hours of the game, I only feel partially closer to making sense of that stuff. Anyway, if you're interested in RPG design, it's a good, quick read. Also, if I may read into this a bit, these guys sure don't sound like they're in the right frame of mind to pick up development and move it to the PS3 for another sequel just yet.
2. Real-time weather design: Unlike in the previous title, Persona 4's time limit for each dungeon was affected by the in-game weather. We did this with the belief that such a system would create the feeling of urgency, since the player didn't know when damage-causing fog would appear.
However, when we implemented it in the game, players were inclined to make dungeon investigation their first priority. Their mentality was, "If I don’t know when the fog appears, I should finish the dungeon as soon as possible." As a result, dungeon crawling and working on the inter-character Social Links, which are equally important, became completely separate and imbalanced.
We tried to compensate by adjusting the weather, in-game messages and story progression, but that created an unexpected workload. A huge amount of data could not be finalized until the weather was set, but the weather kept changing due to our design adjustments.