To more easily get a higher score for bonus missions, start one on Hard difficulty or higher. Once you are actually in the mission, lower the difficulty back to Easy. This reduces the strength of any enemies in the level, but you'll still have the longer time limit from starting at a higher difficulty level. Using this trick will allow to easily clear bonus stages with high time bonuses, leading to a better score.
Nightmare Difficulty
Finish the game to be able to play on this difficulty.