This boss fight is actually fine, it’s just that the player guidance is terrible
By patching it out
The only changes I would've made would be:
At the start of the battle, Amy warns Sonic not to take the direct approach.
Silver has a cool-down of 5 seconds after using his PK directly on Sonic.
Most players find out the hard way they can't just rush in on Silver, so having someone warn the player to take a different approach or a non-direct strategy would help.
As for the PK cool down, that's simply to prevent Silver "pinning" Sonic. It's bad enough he can pin you after losing your rings, it's worse if you're pinned you can't lose one of your rings making the battle softlocked.
If giving the PK a cooldown is impossible, the very least make Sonic's "invulnerability phase" (when he rapidly flickers between visible and invisible) after losing rings immune to Silver's PK.
I'd give Silver a gun.
That's it.
A gun.
By making the mobians in their casual designs instead of their 06 designs
The main problem with this fight is that most players don't know when to go on the offensive, so I'd probably add a hint ring or something that says he can't throw you back while he's lifting objects.
The biggest issue I found with this boss (I never got thrown into space personally, although I did get the infinite ring problem, many times) was with the homing attack—after you hit him his hit box should de-activate temporarily so you can get away. Otherwise it's trial and error working out what you can and can't do, and that kills engagement.
Also, goes without saying, but cut the ridiculous "Sonic Rescues Elise → Sonic Fights Silver → Elise Kidnapped by Eggman" storyline. Either she stays kidnapped or she stays rescued, but the constant changing of hands is woeful.
What do you think?