Dr Manhattan was not bored at end of Watchmen...it was largely his renewed wonder in life that led to his return from Mars, and indeed it was his concern that he was harming others...not boredom...that led to his exile.
If you write him as he was portrayed in Watchmen it's hard to imagine any one less likely to be a villain or play god by stealing ten years from others. None of that...of course...will matter if he needs to be written as a villain. It's brand recognition that's more important here that writing in character.