BJT and JFET have a lot of difference especially their input impedance and their gain.... also BJT is bipolar and JFET is unipolar and a lot of difference arises in speed and noise due to this.... bipolar logic is generally speed but noisy.....
BJT has high voltage gain as compd to FET and FET has high current gain as compd to BJT. also input impedence of FET is very very large as compd to FET