What is this absolutely fine creature that is posed before me

Plot convenience.

Or Eggman doesn’t have enough supplies to make his robots more powerful

Metal knuckles is missing

Metal Knuckles and Metal Tails (not Tails Doll, Metal Tails) were part of Mimic's Film Studios, and were found in a creek. They're both under maintenance currently

Sage is about to take over the empire

Safe is crazy

In IDW Eggman abandoned the Heavies.

As for Metal Knuckles I'd just guess he's outdated and didn't upgrade him to hold up to how much the characters have grown in the modern era like he did with Metal Sonic

It's because nobody at Sega can comprehend them existing outside prequel stories.

^Seeeeeeee THIS is exactly why I miss Archie Reboot