I've always disliked when the relationship causes everything else in the story to grind to a halt. When nothing else is happening the characters just interact in a static vacuum or, at best, a series of disconnected set pieces. I think it's more interesting to see a relationship develop in a dynamic and relevant context, especially because it's a chance to show how the characters handle external influences together.
In a similar vein, I dislike when characters become irrelevant when they aren't part of the main romantic plot. Just because two characters aren't actively trying to bone doesn't mean their interactions lack meaning. A lot of VNs fall prey to this, where characters effectively vanish if you aren't following their path.