First, I'd wish that the genie would not only obey what I say literally, but also what I mean when I say something. Instead of just following the letter of my words, he would also follow the meaning, so as to not have my next wishes turned against me. This is just in case the genie is one of those literal ones.
Next, I'd wish for the power to consciously bend the fabric of reality to my whims. That or powers like Yukari Yakumo from Touhou. Imagine the power to control boundaries and gaps. Not only physical ones, but abstract concepts of boundaries, as well!
... OK, I just want to play with portals and space/time rifts. But can you blame me?
After this, I wouldn't really need another wish, considering I'd be able to use the powers that I gain from my second wish to get whatever I want. If the genie was a nice guy, then I guess I'd wish for his freedom. If not, then I'd use his own powers to lock him away as punishment.