Being able to choose your route and track your general affinity with characters are not mutually exclusive things. Sometimes both features exist together and allow the player a fuller experience by being able to continue to track their progress in the character route or to make a more informed decision about which route to play. =)
If you dislike the relationship metres, though, you don't have to use them at all! They're tucked away on their own screen so players can ignore them if they want. ^_^