A list of real generals would be great, I resorted to taking various Italian last names and "creating" a few leaders to make it more interesting to play, but the real thing would be a welcome addition. I solved to CB problem to an extent, by adding the capitals of all the non-catholic countries into Rome's core province list, thus giving them a permanent CB against that country. As of now, only non-Christian provinces have been CB'd. I'm not sure how to handle the future protestant countries as giving a CB early on would encourage expansion and aggression where it is not warranted, at least at that time. Also, since many of those countries are only 1 or 2 provinces it seems like a huge advantage to be able to march into one and not get the nationalism revolts because of the core province alteration.
Your suggesstions are perfect, in fact I had already implemented most of them, however, I kind of wanted to do something a little different that be completely historically accurate with the scenario. My goal is that the Papal States be a unified papal government with the Pope at its lead and essentially be a crusade for catholicism against any non-catholic heretics

who may rear themselves. But in the end, I do want at much as possible to be accurate.
I have CB's on all pagan and Muslim governments, as well as the whole of the Italian peninsula from Savoie in the west to Venice in the east and south to Apulia. I didn't include the islands of Sicily, Malta, Corsica, or Sardinia because I couldn't see a papal leader ever be interested in conquering those stongholds of catholicism. As such, I limited the CB's to neighboring powers and the heathen.
As it stands now, there are only a few (i hope) bugs that still need to be worked out, but the leaders would be extraordinarily easy to implement, if you don't mind, and as always any feedback or suggestions are extremely welcome.
Thanks for the assistance and suggestions, they are greatly appreciated.