It seems to me there are two broad strategical apporaches to this game:
1. You pretty much ignore the Pope, get ex-commed early on, and go smash up all the armies everyone sends at you. This keeps a nice organised empire, but you're involved in Total War, with everyone.
2. You keep the Pope happy, so you mostly attack only people that are on his shit list, and end up with provinces all over the shop.
Total War option is the easier to play, but I find Happy Pope gives a more amusing game, with much more of the flavour of the historical period.
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