Intakes at the top have a few other disadvantages as well.
You end up blowing the heat from the CPU across other components, and depending on the layout of your board, this can reduce the lifespan of the motherboard's caps. You also end up fighting convective forces by trying to push hot air down, requiring more power from the fans to compensate. Finally, you end up with an intake next to/above an exhaust. This increases the amount of air that's recirculated, and requires more power from the fans to compensate.
You might have a slightly cooler CPU, but it comes at the expense of everything mentioned above, as well as reduced longevity of other components.