What if the genies are bound by laws that don't allow them to be set free? Like we as humans have the laws of physics, gravity, etc, maybe they have some "natural" law that won't allow them to be free. Every creature has limits, mythological ones included. Surely genies would've found a way to free themselves from bondage by now if such a thing were possible!
If I couldn't free them, I'd probably base 1 wish around myself (a selfish wish), 1 wish for humanity/the people I love, and then the last wish for the genie, maybe something like "I wish you were able to live as freely, peacefully, and happily as possible." (which would also hopefully stop it from being able to wreck havoc on humanity lol)