This game isn't a patch on previous war games because

[chunkynut]

It also depends on your current Pope's 'violence' levels. If they are aggresive then many factions will become excomm'd and you seems to get less peace missions from the Pope. At one point (under a aggresive pope (also same faction as me)) all the factions I was at war with were excomm'd (for attacking me a lot) and had a large military campaign to annexe many of their regions that wasn't stopped until the Pope died.

Now I have a placid traited Pope who, as the previously excomm'd factions are now reconciled, has given me 3 peace missions at the same time (for Denmark/Spain/HRE) with the threat of excom or decreased relations even though I have very good relations with the Pope (he's also of my faction) and the other factions do not.

I've only had one general and one priest tried for heresy and executed so far and I'm at least two thirds of the way through my campaign.

I'd suggest trying a faction that A) Isn't Catholic or B) has borders with non-Catholic factions.

[maestro]

I've had loads of occasions where I've thought the same thing - but then I actually checked things out. I'm always getting told off by the pope and told to chill for X turns, then getting really wound up because they're blockading my port and if i attack them I get excommunicated.... but - if I check then there standing has gone down loads, or they've been excommunicated themselves. So yes, the AI can do what they want, but they suffer the same consequences as you.