Being in almost every new game in existance you're on the contrary. Since Amy Rose is a prominent member of Sonic's Team she is definately more of a main character than Shadow has been. Being Sonic's stalker it's abvious and just because Shadow had some roles doesn't make him a prominent in the Sonic series compared to the likes of Sonic, Tails, Knuckles, Amy, or even Cream possibly. It's like saying just because a character like Mewtwo had a prominant role in his movie, more than Team Rocket's vague apperance in the movie, doesn't make him one of the most prominent characters in the Pokemon Universe like the main trainers, Team Rocket, or Pikachu. He is an important supporting character kinda like Shadow is of that type. It's just Shadow has been overhyped to death to see this clearly.
Besides, I remember before Sonic Heroes really put Sonic Team downhill Shadow was meant to be dead. Talk about main character.
PS: From the way the new generation of Sonic is steering it looks like Shadow may be more prominent afterall. Man, I just can't stand the emo hedgehog.