This is a low-detail-resolution issue that is endemic to animation in general, and subsequently, to rendering engines inspired by animation (like most Illusion games). If everyone in a Koikatsu game had different shades of brown or black hair, it'd be a lot harder to tell anyone apart. For a prime example of this, see the game
Sweet Dreams.
That said, it takes a lot of effort to make custom, distinct appearances even in higher detail resolution, and in Illusion game engines, too much distinction between appearances makes the characters look like they're entirely different art styles from each other. So the solution anime (and subsequently, the Illusion game engines like this game's Koikatsu as well as Honey Select) came up with when the faces need to look relatively similar, but the characters need to be distinct, is colorful hair and unique styles. This is also why a lot of these games use uncommon hairstyles like twintails, twin drilltails, twin buns, and so on.
So the tl;dr is: it's best to just get used to it and suspend disbelief about the hair colors and styles, or avoid games using Illusion game engines if you really must have 'realism'.