My suspects so far?
I'm immediately suspicious of Professor Victoria. Never trust a woman asking a detective for help in a detective story, it's almost always a con. (Don't blame me, blame the Maltese Falcon.) But...she's actually kind of a recurring character in these side-story youtube shorts. Would they make her a villain? Part of me doubts it. If it's her, it's more likley to be someone pretending to be her.
Moreso than Knuckles, I feel like Sonic is the one who's acting the most suspicious. He just so happens to have some "free time"? He gets captured by Eggman? Yeah, I smell a setup. Again, if it turns out to be Sonic...it isn't ACTUALLY Sonic. Which, again, seems to hint that there's someone going around in disguise. They DO mention Neo Metal Sonic in the story. And that version of Metal Sonic CAN shapeshift. But...I dunno. They kind of "just" used Neo Metal Sonic in the IDW comics. Would they do that again?
This plot is also pretty similar to the plot of the Chaotix 30th Anniversary Special comic. And in that issue we met a new thief character who uses disguises, Enigma. That'd be kind of a deep cut. But, maybe that was a bit of early cross-promotion while this was in development? Maybe the plan was always to have Enigma be a new Chaotix-focused villain?
Part of me kind of wonders if they'll bring in Mimic from the IDW comics? He's a villainous shapeshifter that would work well in this scenario. I just don't know if they'd use anyone for this audio drama that comes from the comics. Outside of maybe Tango and Whisper. Maybe that's more history than they expect a casual audience to be familiar with. But, a shapeshifter villain would explain any "inconsistencies" in various character's personalities.
Or it could be someone new. Espio did talk about how he felt like his skills were getting rusty. Was that just a character focus moment, or was that foreshadowing him having to face another ninja chameleon later on in the story? Or Charmy's horse...could be a horse of GREAT EVIL! (Say it ain't so, Sir Connery!) Or maybe these "Astroscopic Lenses" are one of those ancient artifacts that are actually ancient tech with a AI inside it, and it "stole" itself? I could see them just making up someone new as a one-off villain. This franchise likes to do that, in it's spin-off media.
So, we'll see how this plays out. I'm not expecting this to have a serious ending, because of the tone. It's probably going to end on a bit of a gag. But, we'll see.