The movies were split between two discs in order to maintain A/V fidelity. I know its annoying to have to switch discs, but I would much rather have to do that as opposed to viewing something with less than optimal A/V quality. I do agree that combining the supplement discs on to fewer Blu-rays would have been better though.
With the exeception of some strange color timing choices in FOTR, these discs look and sound great. Spreading them across two discs allowed them to allieviate some of the compression artifacts that were present in the theatrical cuts.