What Could Have Been: At one point, it was intended to show Maria's death, rather than cut away as the player hears the gun shot. It was decided that including that would make the game too dark & the age rating would have to increase, so the decision was made to cut away from the flashback instead.
Apparently, SEGA got a letter from a young fan saying how cool it'd be for Sonic to have a gun. SEGA, wanting to expand their audience, thought it was an all right idea, but thought that the gun-play wouldn't fit Sonic's character, so they gave the role to Shadow.
Before everything was toned down to fit into E-10, there was a lot more swearing, including Sonic saying "Piss." In the final game, Sonic only swears once.
Word of God: SEGA says that the Pure Heroic path is supposed to be canon. Given the events of the Last Story, this is slightly doubtful and has caused much confusion.