I read changing the options will screw the game up when you play Magna Mundi. Something about balance or so. So basically leave them alone when playing MM. In regular NA I prefer to play the game with every setting on default. I do play with historical leaders and monarchs in 'scenario's' (i.e. Revolutionary France or so), which can lead to frustrations. For example, my sizeable fleet of 110 ships or so had this brilliant admiral but when he died, the fleet was ripped to pieces and I couldn't recruit a new one, despite having 100% naval tradition.
