It's basic hydraulics, the larger the master cylinder bore in relationship to the caliper and/or wheel cylinder bore, the higher the pedal pressure and the shorter the pedal travel. Generally installing a larger bore master cylinder than what is needed gives you a raised pedal pressure and the resulting shortened pedal travel makes pedal modulation more difficult. Good pedal modulation gives you finer control of application pressures, resulting in a better ability to keep from locking up the brakes unnecessarily at heavier application pressures and better control of wheel lockup at the limit.
While arbitrarily going up in master cylinder bore size from stock without a respective increase in the bore size of the caliper and/or wheel cylinders is probably not something you want to do as a rule, going down on master cylinder bore size slightly will help reduce pedal pressure at the expense of more pedal travel and give you more control over modulation. It also allows drivers of slighter stature to work the brakes without fatiguing as quickly, especially without adding a power booster of some sort.
Different manufacturers have guide lines for how much the pedal should be above the floorboards, but the key is getting a master cylinder that reduces pedal pressure and will still lock the brakes up firmly without letting the pedal get dangerously close to the floorboards.
If design considerations (size and type of the wheel brakes, size and weight of the vehicle, distance to the floorboard, etc.) don't allow the pedal travel needed for a particular bore master cylinder in your situation, then a larger bore master cylinder must be used, even if some sort of booster is needed to reduce pedal pressure.
If you liked your stock one, replace it withthe same.
