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Cross-Dressing Voices: Surprisingly, Jun in the English version. In the Japanese Innocent Sin, he is given a very deep but reserved voice. When a replica of Jun is faced as a boss in Eternal Punishment, he is given the voice of a young girl in the English dub.
No Export for You: The original release of Innocent Sin was never released outside of Japan, whilst Eternal Punishment was also released in America. The Innocent Sin remake for PSP was released worldwide, but the Eternal Punishment remake has not been released outside of Japan, making it the only Persona game never to receive a release in Europe in some capacity.
Wes and Tatsuya are both dark, brooding male protagonists of a similar age.
Rui and Lisa are both the male leads potential love interests who realize the connection the male lead has to the villains.
Nett and Maya are both ordinary people trying their hardest to get behind the supernatural events.
Bitt and Eikichi are both people who often end up in dark, small places and have a small group of friends.
Megg and Jun are both people with close ties to said investigator.
Secc and Yukino are friends with the investigative characters, but leave the plot about halfway through.
Orre and Sumaru City are both regions where everyone knows something about the supernatural goings on.
Es Cade and Philemon both help the protagonists and are ultimately part of the problem.
Team Snagem and the Masquerade both used to be relatively good, until around the time the male lead left.
Cipher and the Last Battalion both make the aforementioned organizations even worse and take over when they stop operating.
Pokemon XD and Eternal Punishment both pick up where the vague endings left off, in a Lighter and Softer world, where the events of the first are generally ignored outside of legend, in order to finish what was started then.
What Could Have Been: Supposedly, it was planned that you can influence Joker's One-Winged Angel form by spreading rumors that the Joker is like an angel or like a devil. The NPCs that reference this are still in the game, but it doesn't result in a rumor.
Word of Gay: A lot of this. The scenario designer, Satomi Tadashi, supports the pairing of Suou and Kurosu, and he even managed to change the character designer's own opinion of the pairing in one conversation. And let's not even go into detail about the drama CD, whoa baby. Baby chickens are a really big deal.