Irrational Games didn't develop BioShock Infinite with the intention of making BioShock in the sky, because it thinks that'd be boring.
Many first impressions of BioShock Infinite saw it as "BioShock in the sky," but Irrational Games disputes this idea and went over the game's development process at PAX East 2011 to prove it. Irrational explained that the intention was actually to make a game completely different from BioShock so the studio would be able to stay interested.
The Irrational speakers, which included Ken Levine, Nate Wells, Shawn Robertson, and Stephen Alexander, said that they'd be "fucking bored" with a game that was just BioShock but in the sky. Irrational likened the comparison to calling a Buffalo a "large racoon." Sure, some elements are similar between BioShock and Infinite, but the development motivations were and are so much more than that simple concept.
Infinite actually came about from the desire to create an alternate version of the turn of the 20th century. At the time, there was an incredible amount of optimism about technology, and America was transforming. The changes in society, along with the style seen in advertisements and architecture, were huge inspirations for BioShock Infinite.
Another big change Irrational wanted to make was to use the environment as a gameplay device rather than just something pretty to look at. Players could stare out through the glass walls of Rapture, but the fact that the city was underwater didn't have all that much of an effect. In BioShock Infinite, being in the sky means something. Platforms move and shake while the player hangs from the game's skyline system, on the verge of death at any moment. As Levine says, it's "like being on a roller coaster while hanging in the air, and you have a fucking gun."
Art direction-wise, BioShock Infinite has also taken a different turn. Irrational showed the evolution of the game's concept art which started very dark, and eventually became the more colorful world we see today. The studio says a brighter world can be even more alarming than a dark one, pointing to the lit scenes in The Shining as a comparison.
Because of these factors and more, Irrational doesn't feel that BioShock Infinite is a replica of BioShock. At the least, it wasn't developed with that concept in mind, and Irrational hopes it will instill different feelings into its players.