The whole purpose of that storyline is to show us Nate out of his character. To give responsibility to a character who typically only thinks of himself, and in the end to once again show how unhappy/selfish of a guy he really is, i think. Brenda does come back into the storyline, and the Nate/Lisa is actually very cruical to the show overall.
Stick with it, i actually think the Season 3 finale is one of the strongest episodes of the series, very beautiful and I'd love to hear your thoughts on it as it keeps going along.

3 ends with a major plot development, but I felt that season 4 was the weakest.