One interesting aspect of missions in MTW2 is that they won't be only given by the pope. U'll get missions from the noble concile of your own faction, the guilds installed in your towns and other factions as well. Meaning, there will be some choice to make as what to do first.

I guess some conflicts between your allies will eventually emerge from your own decisions, just like it was when monarchs had to make changes leading to war with old friends in order to get more powerfull allies.