As mentioned before, 100% is really hard to hold, since you lose a substantial amount of it on ruler death. There used to be a ruler decision that granted missionary strength for high stat rulers, but that was removed from the game. It was replaced by a new event chain, in theory, you can get +2 missionary strength modifier from this event chain, but it is rather rare.
But yeah, missionary strength is a pain, especially since the most undesirable provinces, heretics, are some of the hardest to convert because of the -2% missionary strength.