The key problem is splitting it into three movies. Two was stretching it already. The Hobbit, even with some of the new stuff (White Council, Dol Guldur) added in, shouldn't be longer than 3 and a half hours. Nine hours is far too long.

The over-reliance on CGI and desire to push boundaries (48fps; 3D necessitating new ways of shooting the differently-sized cast) - two things the prequels fell victim to - don't help much, but the main problem was splitting up such a thin story over multiple films.