I feel like it's simple math.
Sonic 1: 2 cartoon characters (Sonic and Eggman)
Sonic 2: 5 cartoon characters (Sonic, Tails, Knuckles, Eggman)
Sonic 3: 7 cartoon characters (Sonic, Tails, Knuckles, Shadow, Eggman, Grandpa Eggman)
By Sonic 3, they can leave the human cast behind, because they have enough cartoon critters to carry multiple plots. Sonic 1, they had to work with what they had, and it wasn't great. And, honestly, I feel like the humans in both 1 & 2 leaned into "wacky hijinks", it just didn't work because of course they are going to pale in comparison to their cartoon compatriots.
Of course, if I know anything about Sonic fans, it is that people are going to start complaining about too many Sonic friends soon enough...