Shadow without a doubt has a bigger fanbase than Knuckles but Knuckles has a much smaller hatebase. There are some Knuckles haters out there for sure but popular opinion is either "Shadow is Awesome!" or "**** Shadow! Why do people even like him?". Personally, I think it would piss a lot of people off if Shadow was in PM or SSB4 instead Tails or Knuckles but I'm sure just as many people would start jumping for joy.
Not trying to be a jerk here but honestly, if the PMBR did decide to put more characters in (and that's a big "IF") I don't think Amy is a likely candidate. There are only 5 spots to fill. Tails would obviously be the #1 Choice for a Sonic rep, MAYBE Knuckles, and BEST scenario both... Idk man. It could definitely be done though.
This is so people know who you are talking about. I had to really fish for this.
(The Legend of Zelda:Spirit Tracks)