I would set myself up like Vetinari from the Discworld series. My official title would be Tyrant, and I would run my country (if not the entire world) with a well padded iron fist.
All of my subjects would be free to do whatever they wanted, they could run their own business, choose where to shop, visit or move anywhere they wanted, and of course they could still lie, cheat, steal, and swindle. The biggest difference is it would be very much a bureaucracy. The swindlers would keep track of who they swindled in very much the same way the business man keeps track of his finances and taxes.
In turn, the businessman could only be stolen from a certain number of times a month, for a certain total a month. Any thief who goes over that amount would be forced to return the overflow and get put in prison for a specific length of time.
I would also strive to make myself irreplaceable as a leader, to where people could say, "Yeah he's a tyrant, but at least stuff gets done. Who knows what would happen if someone less capable was in charge of all this."
And of course my scientists would be some of the most sciency-scientists in the world. There would be an entire branch of science for creating and dealing with strange and possibly controversial topics. After all, if they have a reason for building a giant rabbit-sundae-with-whipped-cream-and-a-cookie slinging catapult, who am I to stop well documented science?
