SP, Shadow is the second most popular Sonic character behind Sonic. He used guns, but that doesn't stop him from being a Sonic character with his own unique moveset. He just has weaponry skills with his moves. He has an established backstory, and has plenty of melee moves.
Now yes, Knux deserves it as well, but I don't think they one or the other deserves it more. I would honestly push for them both, if possible, but it doesn't really matter now.
Now I think most Sonic fans don't mind you bashing Silver. Hell, I'm a huge Sonic fan but ****...he's an unestablished tacked on character. It seems Sega was yelling at us "RESPECT AND LOVE SILVER AS MUCH AS YOU DO SONIC AND SHADOW! NOW! HE'S COOL BECAUSE HE MOVES STUFF! WITH HIS MIND!" So yeah, they;re REALLY going to have to redeem him in a later game for people to care about him, since he was so friggin forced...but seriously, lay off Shads. He's well established, and well liked. I understand you're upset about Knux, I am too. But no need to bash at other good characters to use make a good argument.
...Except Silver. Amy should of been in his place in that level, she's been around longer and stuff.