FETs tend have larger input impedance than bipolar transistors, and the gate of a FET typically draws much less current than the base of a bipolar transistor. So if you have an application that needs lots of transistors and you don't want to draw too much current from the input, you might want to use FETs. FET transistor parameters are also less sensitive to temperature and the response is more linear. But they are also more sensitive to static. In practice, there are many considerations for circuit design (including cost).