All of the things you mention - being excommed, Papal reemergence, vices, and province rebellions - seem to me to be designed to slow a player down and make the game more difficult.

It is, as you say, a worthy successor to Shogun, but there aren't any cool vids, like the STW ninja movies or an ending.

Be sure to try the Viking Invasion Expansion. There are many good mods, I like the STW for VI mod.

ichi