Have you noticed most of the "didn'ts" you mentioned are strictly 2D platformers or spinoffs?Sonic Adventure 2, Sonic 06, Sonic Unleashed, Sonic Generations, and Sonic Forces all did this to different degrees, but it's not as much of a trend when you consider that since Adventure 2 did it, Sonic Advance, Advance 2, Battle, Advance 3, Rush, Rush Adventure (Minus the vehicle sections), Secret Rings, Black Knight, Sonic 4, Colors, Lost World, and Mania all didn't do it much if at all.
This is what I mean when I say "mainline". The games which do split the game into different gameplay modes are ones which follow the Dreamcast or Unleashed gameplay formula; of those, Colors and Shadow are the only deviants.