Your papacy ideas seem great, keep running with 'em.
As for the discussion on discovery, to me it's a matter of what comes most naturally. I personally haven't a clue what XML coding would be necessary for either. Just by the sound of it I think Arbitrary's idea is more interesting than Epic's [while his likely being less strenuous to implement] , but that's not to say that it's a bad idea. Either would be great and whichever one ends up in the mod I'll be happy. It just seems too easy to build three galleons and pay some money.
As for corporations, you could add the East India Trading company and the Hans. League, among others.
The random events have limitless possibility to make the game more challenging and interesting, so borrowing many from EU3 and inventing new ones seems like common sense. Also the Magna Mundi mod for EU3 seems to have a great deal of good inspiration.
IMHO, your extended 10x4 civic section would help add even more depth and allow for more tinkering to occur. The only difficulty I see with implementing it is balancing and making each civic different enough from other. I suppose my preference with expanded civics is I like options. Again, Eu3 has a great deal of ready inspiration.
Creating all the Civics might be a bit of a chore, but it's certainly possible and as usual I'll pipe in when I think of something.