Amy showing that she's serious about her love for Sonic. "If I had to choose between the world and Sonic, I would choose SONIC!"
Elise's line in the ending that she doesn't care about the world (compared to her friendship with Sonic) is clearly meant to echo this. Unfortunately context casts her in a more negative light as far as the fandom is concerned.
Sonic and Elise's reunion, just before he fights the Egg Wyvern.
When Elise revives Sonic.
... which is followed by a heartfelt thanks from Sonic.
Something of note in the Japanese version: throughout the game, Sonic usually says "Thanks" in English. He doesn't here.
The final cutscene, After Elise blows the flame out, supposedly guaranteeing that they would never have met and won't have any memory of each other whatsoever, then Sonic arrives to the festival we see at the beginning of the game, when she causes a wind to go past Elise, she shows a sign that she might still remember Sonic afterall.
...which is followed by a shot of Sonic smiling down at Elise from afar, giving us the freedom to believe that Sonic remembers Elise too.
The beach scene with Team Dark. Really shows how tight knit a group they are.
Near the end, when Pokecapn really cannot withstand this game anymore, the other goons take over until he decides that he can, assigning themselves characters. Pretty much summed up with KFJ's exclamation of "Aah, teamwork!"
When the game is finally over, the four remaining members of the group read through the end credits in order to find out whose "fault" the game was. Many vocal critics of the game tend to be irrational when talking about it, bashing every little aspect and calling for the heads of everyone working at Sonic Team or Sega in general, but the gang makes an honest effort to discern between those who should and shouldn't be blamed for the poor quality of the game, and they even pity the team members who had to make tough decisions and deal with pressure from those who were truly at fault during production. It also showed that the "healing" had already begun; despite all the angry shouting and apparent Sanity Slippage during their playtime, the crew were all still friends and able to make rational judgements without lashing out, which is more than you can say for most internet Sonic fans.
So we can basically say that about 80% of the staff on this game are good people, and they did good work.