The fun, fast Sonic or Tails levels get dragged down by the slower Big the Cat or Knuckles stages. Sonic Adventure is one of the first games that come to mind.
Even some great 3D Sonic games suffered from these issues. In terms of gameplay, those characters screw up the natural flow of the game. For the story, the amount of furry friends makes the plot a mess. One big issue is the amount of characters.
That’s why something like Sonic Boom just doesn’t work, there is too much going on.