I agree. They are all relevant in the books. Not all information relevant in the books would work well on film. They are two different mediums.
However, for example, the Ring was supposed to have an unyielding temptation to whomever holds it. Tom Bombadil was able to play with that ring and it had no effect on him. How could it be explained, so the movie goer could understand that Tom was another force of nature, which is why the Ring had no effect on him?
Probably the only storyline missing that could have been told in a way that movie goers would understand was the scouring of the Shire. This could have been told in small ways, across the three movies, until their was a big buildup towards the end.
But that is really the only story line that could have been worked into the film, I think.