It seems that there was a disconnect or upheaval of some kind between the times of the Geonim and the times of the Rishonim and the hakhamim that these two eras contained. Shittoth regarding tefila, berakhoth, kashruth, and other areas seem to have been practiced in a completely different manner until many Rishonim came along and views things differently.
My question is: "What happened? How their understanding of halakha be so different? Further, how could the Gemara and other literature be viewed so differently between them?"