The group infighting as a whole I didn't really like. It didn't make much sense. The entire game was spent with them overcoming their past troubles and trauma and unifying as a team. Then a shiny magic key comes along and *BAM*. Everyone starts beating each other up. The groupings may work overall, but the setup is weak.
Also, the setup for the time travel is weak. It just suddenly pops into existence at the start, and then shuts down at the end. No foreshadowing, no explanation, no real closure. Just voila. Time Travel.
Also, it makes Player Choice of romance options pointless, which I also hate.
I once read a fairly complex essay listing a ton of minor things that were hinted or showed themes trending towards his survival. I wish I could find it again, but it was something I read about five years ago, and I have no clue where it was. There's also the heavy stress from Ryoji in the chat with SEES after the victory that Minato wasn't going to die as a result of the battle, that's like 90% of what he's saying there. It may have been a theory, but I felt it was open enough to leave it a choice.I'm going with Scott_ffgamer here and say that the ending really paints the fact that Minato is not doing well in the ending so I have a harder time interpreting the "happy" ending you envisioned. Granted I didn't pay attention very well my first time through and thought the same as you, but after playing the game a second time through I caught the more sinister implications of the games ending. The Answer simply confirmed my suspicions and I honestly feel its grown into one of the more intriguing subplots for the series, though I'm still waiting for IS Tatsuya's parallel world to come back and bite the series in the ass as well but that may never happen. I alos feel that Minato's death works for the cast of P3 because they relied so much on him that when he was gone they were left to finally make the hard choices themselves and that to me represents that we the player are suppose to also walk away from the game and apply its message of making the most of our lives everyday.I hate the way they changed the ending. The ending of Persona 3 was ambiguous, and deliberately so. Minato's fate was never declared. There were indications feeding both way, that he survived, that he died. You could take it any way, and have plenty of evidence supporting you (Ryoji: "Don't worry, time will continue for you, and for him". FRELLING LIAR!). It did, in fact, feed back into the entire theme of the game and the series: Hope versus despair, with freedom to choose being the determining factor between which fate awaits in the end.
The original ending was nearly perfect. The battle was one, but at the cost of the team's memories and friendships. Only Minato and Aegis remembered. Until the day of the promise, when they all remember, and join together. It was upbeat and hopeful. The Answer renders THAT reunion kind of pointless, since they just meet back up to beat the crap out of each other for contrived reasons.
There's also the fact that I find it kind of hard to believe that Mitsuru would let him die (especially if you romanced her). I think it more likely she'd take him to a hospital and keep him on life support indefinitely (not that I think it would matter, I highly doubt that the death of his body would stop him coming back if the seal was no longer needed). The way she did, say, Chidori.
However the biggest issue, is that taking it as a death, I think the actual execution of the death scene was absolutely sublime in Persona 3. The fade to white and peaceful drift to eternal sleep, with dreams of friends floating through the clouds during the credits was absolutely frelling brilliant, and I felt that The Answer's handling of his death really marred that. The battle with Erebus and the reveal of the Great Seal was fantastic (easily the best part of the entire Chapter), but I felt that discussions and explanations of his death after that were just unnecessary, and blighted the overall work. Their content may have been the same, but the presentation was incredibly lacking by comparison.