Hmmm, I have been thinking some more about sects, and I WOULD still like to see them in but, instead of being able to choose them from a list, sects would instead appear in a semi-random fashion based on certain in-game factors! For instance, a heavily militaristic civ, with a long history of warfare, might have a small 'blood-cult' emerging in certain parts of the nation. If this sect starts to take hold, then you might be given the choice to 'adopt' this sect as the state religion. Certain CORE religions would be much more likely to generate certain sects over others. For instance, Monotheism would be more likely to develop an Orthodox or Reformist sect, wheras a Non-Deist or Animist religion might be much less likely to develop either of these sects.
So, the factors which might determine the emergence of a sect might be your civ traits, your 'ethics', degree of happiness and corruption, your core religion and your unit, improvement and wonder choices!
I think it would be wrong to ignore the importance of sects in religious history-after all, The Jewish Ascetic sect known as the Essenes are believed to have been a major contributor to the actions of both John the Baptist AND Jesus. Similarly, the Catholic Ascetics of Southern France (the Albergienses) posed a very great threat to the authority of the central Catholic Authorites. One also cannot overlook Christian sects like the Orthodox and Protestants, or the Wahaabi, Sunni and Shiite sects of the Islamic faith. This importance I feel just can't be accurately conveyed with the core religions alone!
Oh, one final thing I should point out is that, as daunting as that list as possible religions might look, it is important to note that many of the possible permutations will not be available due to isolation of culture groups. After all, on a real world map, the Western Europeans won't meet the North/South Americans for thousands of years-precluding these culture options from European civs!
Yours,
Aussie_Lurker.