I don't like the fact they pressed so hard for Naoto to accept the entire female sex, as that is a bit more of societal conformity, but Naoto is perhaps the most interesting character for me due to the depth of their character. I disliked Persona 4 overall compared to the other persona games, but Naoto put a smile on my face.
Naoto Shirogane, hands down.
Yeah, P4 cast is out of the picture.
As awesome as Futaba is, she has no feats that support her ability to hack into high military grade robotics. Cracking into television networks isn't comparable to a literal war machine. Additionally, her taking out fake hackers doesn't add to this either. No doubt that she is remarkable, but game accomplishments just doesn't come close to justifying that claim. Additionally, persona evolution is just a symbol of their resolve, not necessarily their actual power. Joker doesn't do anything that P3 MC hasn't done so I still don't see him as better. I still admit he has better physical stats than p3 MC due to gym and personal exercise, but his persona feats don't really compare provided the canon.
I think P1 and P2 teams would ultimately take the spot, but in the newer age of the series I vote Persona 3 SEES as the most powerful. Compared to p4 and p5. SEES had actual skills across the board, where each member could take out their respective counterparts in p4 and p5. I do admit Naoto Shirogane is an exceptional team member from the p4 cast.
P3 MC is also superior to Yu and Joker in all regards, with and without the ultimate arcanum. He is a master in all weapons (except firearms). I do admit that Joker is likely a lot more agile though. Yu just doesn't compare to either though.