Seems like Eugene would be happier with Negan. Everybody in Rick's group took him for granted, and the only person who gave him encouragement, Abraham, isn't there. He didn't fit in.
With Negan, he has comfort and status, and his abilities are being put to good use. He's also allowed to do what he's good at and not get pigeonholed into fighting.
At this point, I don't see much point in him playing a long con.
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