You make a fundamental assumption in your post; everything that happens has to help fight the Shadow. You have to remember that WOT is not only about good vs evil but about the whole world. So its justified to have a 'pointless' plotline which deals with a character's personal story.

Why was it given so much prominence? Because Egwene needs it. Why is Egwene so important? Because she makes for good reading. Remember a author need not need any other reason to have a character other than the fact that she is fun to read.
The Tower story also deals with recurring themes in the sries (such as the theme of reversed power).

Why was the plotline so long? Because Rand needed the split in the Tower to begin and ed at just the right moments. (others have already posted extensively about this).

Finally why was there so much about the Tower in TGS? Because
1. such a long drawn out plot needed proper resolution
2. it served as a good symbolism ad mirroring tool (Rand's descent into darkness vs Egwene's shining example).
In fact I believe that Mat's and Perrin's plot lines will also be given as much or more prominence in the next book. So its not really a bid deal that half of TGS was about the Tower.

SO, in conclusion, the Tower split was an important plot device for Rad, served to bring out a main character, pointed out important symbolic themes. And above all it was just a good story