Apple apparently moved the iPad 2's microphone to the top center of the device, and that's causing problems in performance across the Wi-Fi and 3G models, says iLounge. The 3G model's mic is set in a different material than the Wi-Fi version (because of the extra antenna), and that means that the Wi-Fi version sounds "markedly cleaner" than the other versions, with the CDMA model sounding the most "slightly muffled and echo-prone." The problem is reportedly exacerbated when the mic is facing away from its target, like when you're using the iPad for FaceTime.
I doubt this is a deal-breaker for most users, but it is probably something we'll see fixed in the next version of the iPad. It's interesting that this either never came up during Apple's testing, or it did and the company simply decided that it was good enough to let slip by.
Meanwhile, if you need a nice clear microphone for your 3G iPad to use, there are other third-party solutions to check out as well.