I think Amy's (mostly) grown out of the annoying kid shtick in favor of being the feminine character, but otherwise yea this. Keep these characters to the spin-offs/comics, if you ask me. That being said, I'd be fine with having these copies show up in the main game every now and then as fanservice, sorta like Mania Plus with Ray/Mighty.
The problem isn't the existence of the characters themselves, the problem is the worthless writing that denies them a purpose or place. Either have Silver be around permanently or don't. Either have Knuckles guard the emerald or don't. Let Shadow be able to acknowledge his past because we spent THREE GAMES dwelling on it. Just fucking... commit to telling an actual story or don't. Just commit to anything. That being said, the Deadly Six can dry up and float away forever.
I would honestly just abandon Shadow, I don't believe there's anything that should be done with him story-wise. Also the Deadly Six, but that's a given. ...I'd like to suggest a different ideology for Sonic spin-offs, however, particularly those that have little to no story: bring back every dead, one-off, or otherwise unaccessible character lmao preferably in order of most popular tho, wouldn't want to get elise over gamma or something