It's almost unanimous that Shadow's story may very well be the best of the three storylines, according to what people have been saying about it.
I thought it was funny, too, regarding Silver, being able to fly so long in the cutscene but not able to do that in the stages. :P
Sonic's death was... eh.. it was meh. On one hand, the way it was done, graphics and reactions aside was pretty good, IMO. The flaws, though, are hard to miss. First off, there are only characters to show true sadness over Sonic's death, whilst still remaining true to their character.
Tails: I kinda expected him to show more emotion considering what happened in previous games and considering their bond together.
Knuckles: I just hated his face throughout the entire game. And his line, "Sonic!" with the face he showed... Nu uh, didn't suit him.
Amy: Pretty well done I guess...
Silver: He shows more signs of remorse than... oh let's say, Knuckles, when Silver just met Sonic! :S Anyway, I liked his lines and his attitude towards it.
Shadow: Probably the best. Could hardly look at Sonic without getting upset.
Rouge: It was okay I guess.
Omega: Just.. no. :P
Eggman: Even he showed SOME signs of sadness so I guess what they did with him was pretty well done.
Aside from the reactions, the cutting and other stuff was somewhat...well sloppy.
I laughed when Knuckles ran the wrong way at first when they all left to get the Emeralds. So jokes.
I think I understood the time-space rift stuff and Solaris pretty well in terms of story but I don't get how Amy, Tails and Knuckles survived. It's not like they had a Chaos Emerald like Shadow, Rouge, Omega (not one each) and Silver did. Weird but anyway...
One pet peeve about Silver's ending sequence is the music that was played. Remember, F-Man? He even commented that it sounded like music that was played during a Disney movie or something. But seriously, the scene was so emotional and it didn't suit it at all. I liked the rest of it though.
Also, I knew F-M was gonna say some sorta smart-allic remark. ;)
I'll mention some other scenes in the next post. I'll start with Sonic's then work my way through. Just some highlights I guess.