Yes, you could make a Simulacrum of another creature, even an unwilling one. The spell doesn’t require a willing target, saving throw or spell attack. Merely that the target is within touch-range for the casting.
You don’t even need Wish for this; if you can somehow keep a creature in place for 12 hours you can already make a duplicate of an unwilling target. (For example because they are sleeping, knocked out, imprisoned, or in a coma)
Wish just makes it a lot easier because the casting time is so short. But nothing in the Simulacrum spell prevents its use on hostile targets. You’ll end up with a duplicate of your enemy except they’re friendly to you and have half of their hit points.
(Keep in mind the spell does not say it also knows everything the original knows. If this was a plan to steal a secret from them, it might not work.)