You do have a point I can't deny that.
But criticism is inevitable, there will always be angry fans and mean critics. No matter how good somethin might be, someone somewhere will hate it. Sonic the Hedgehog (2006) is almost the most criticized game on Earth and some people still play it.
My point is, many people as I know, want these little creatures back, and havin them wouldn't be a mistake to them, you're sayin they deviate from the Sonic gameplay, Blur is sayin he sometimes gets bored from what you called the Sonic gameplay, and this is normal because people are different, if you get bored of Sonic games you'll play somethin else, but if Blur gets bored of them he'll raise a couple of chaos.
The solution to this is really simple, if you like Chao Gardens go to them, if you don't you can easily avoid them, skip them and play the game normally, the story will not be affected in anyway.