Like all long routes, the two directions provide entirely different walks: only the accommodations are the same.
Most guide books describe the route from Ilkley to Bowness, though the Cicerone guide by Terry Marsh features both directions.
Positives in my opinion are:
The twisting-turning miles between Burneside and Crook of Lune are behind you early in the walk, which is a good thing for me;
The views of the Howgill Fells are better;
The views of Ingleborough and Penyghent after you climb out of Dentdale are better;
Transport options from Ilkley are much better than out of Bowness.