I remember MTW and the Pope. Not much happened really and it was a bit of a let-down. There were hints of events that would affect the game hugely such as excommunications and the downfall of the papacy etc. But nothing much happened.
I read somewhere that there will be more integration by being able to rig elections etc. which is good but I think they can take a few steps more.
If the Pope is overthrown then as a good catholic leader could you not ceed him one of your provinces and help to put him back in his place? Instead of the Pope showing up again everytime (in MTW) a few turns after you take Rome, this would add more depth to the game. It would also give you a side-plot to the game to focus on which would be nice.
By ceeding the exiled pope a province you improve your loyalty to the church and gain bonuses. Plus if you manage to reinstate him to Rome you gain his ear (or control).
I would also like to see the possibility of putting one of your bishops forward if the Pope dies. That could gain you another huge advantage if you are the English and the new pope was one of your bishops. You gain an ally, crusades become cheaper, you don't have to pay so many tithes, or you can control (to some degree) who gets excommunicated.
Finally also I would like to see the idea of multi-faction crusades. When Richard the Lionheart went crusading the French and HRE joined him. But they didn't suddenly all become English. I want to see crusader armies controlled on the campaign map by the faction that started it. That faction can offer other factions the chance to join the crusade and send troops. On the battle-screen each faction's troops are controlled by that faction, not given to you as reinforcements.
Hope I explained that well.
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