You have to use some strategy. There are some tutorial videos on YouTube (no h-scene obviously) that show what to prioritize upgrading at different times. Some advice I can give is that at lower health values, the enemy will receive a debuff in movement and attack speed, so unit health isn't everything. You also get more points for getting more hits on them each attempt.
Also, I recommend resetting progress on an enemy if you go over the number of attempts shown at the start of each one, as you need to get all stars to unlock the bonus stage.