Juku is correct, you don't really need to finish any of the sidequests or even all the cults. Promo III requires some progress on some path (Cyberweb, Underwater, Caves, live alien). But for a smooth game, most of them include good prizes and you should deal with them. For example, the ghost missions give you stunning weapons which ignore armor, which are really useful in dealing with more difficult MIBs and obtaining good armors early. Also, for example you get the best transformation, Spartanism, out of eliminating the syndicate and also a decent one, Kyberos, from dealing with Dimension X.
