refined mechanics would include
- casus belli system (prevention of random war)
- more reliable and polished pope favor chart (maybe even updated as frequently as the map)
- an actual track of time
- changed rules
- more deliberate warfare and expansion
- turn limit (you can either expand, build up your army, or something else [but not at the same time])
- science will be a lot more difficult as a result of the dark ages
- religion, missionaries, and inquisitors will play a much larger role
- religious tenets (religion will act similar to ideologies, if that's how you'd like to visualize it)
- papal doctrine and jihad doctrine updates
- crusades won't be as op or frequent
- jihads won't be as useless
- subdivisions of religion
- ability to found new religion
- code of chivalry
- natural disasters and random events
- 99.99% accurate faction list
- etc
most of this will be carried over to any other rp I do (the ones applicable, at least)