That I feel is easy to work around.
"With the Raft being proven to be ineffective to the containment of holding supercriminals, Empire Unlimeted proposes a new system to confine them." What really matters is that he gets superpowers, not really that they come from superheroes.
As for not leaving an impression, characters gain more notoriety the more they're used. Simply keeping him in limbo won't improve his character. It's through continued use that bland characters like Doc Ock, Green Goblin, and Kraven the Hunter rose to prominence.
This reminds me of Regent turning up in the Marvel's Spider-Man cartoon. It seemed kind of random aside from him being a Slott character.
My guess for the next Miles game villain... I'm not sure. It would probably have to be someone with minions to facilitate bases and/or add flavor to the boss fights. I don't know if Miles has many crime boss style villains, but I can maybe picture the Assessor or Techno Golem.
I could see Assessor working, but Tomoe would probably be too close to Tinkerer to use.
Yeah, who else does Miles have? They can't use Ultimatum as they can't use the Avengers, whose powers he stole. Regent's out of the running for similar reasons, he doesn't work when there's no non-Spider heroes to capture and power copy.
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Ceres, Sinister Syndicate, Assessor, both Bombshells, Sandman, Hobgoblin
I think there's probably a better likelihood of taking one of Peter's lesser prominent main villains to use for Miles.
Ceres would be too similar to Tinkerer, besides she's not really a physical threat.
It was a waste to not use the Bombshells but they probably didn't want to pack the game too much.
Sandman will probably appear in the next Peter game.
I don't think this is going to be another instance of Hobgoblin appearing before the Green Goblin does, so we'll have to wait for that.
One thing I was hoping that this last game was going to do was adapt the Roxxon storyline from the Ultimate Comics, with them being (in)directly responsible for the powers of Miles, Cloak & Dagger, and Bombshell.
The artist formerly known as OrpheusTelos.