Whether you choose a floor stapler or a cleat nailer can simply be based on personal preference. Maybe not as personal as "briefs or boxers," but for the most part, both machines will do the job.
It does appear to be the consensus, though, that cleat nailers have a slight edge when it comes to extremely hard and brittle woods. For example, we're finding that many bamboo floor manufacturers are deliberately specifying cleats to try to keep tongues (the part of the flooring that fits into a groove, to help boards lay flat next to each other) from splitting.
Here at Pete's we're usually stapler people, but we deliberately carry both types of floor fastening machines since they each have their advantages.
Both cleat and nails will work well on American hardwoods. But if you have a Brazilian cherry, Brazilian walnut, or bamboo floor, we're going to steer you toward the Powernail 50P, a cleat nailer. Why? Not only because she is a cleat nailer and less prone to breaking off the tongues of those more brittle woods, but also because her cleats are 18 gauge, which is slightly finer than the 15 gauge legs on our staples.
Here's the summary:
Choose a cleat nailer for very hard and brittle woods, like Brazilian cherry, Brazilian walnut, or bamboo.
Choose a floor stapler for any wood that is not very brittle.
Both tools are great for American hardwoods.