Mostly NIMBY problems that apply for the repository apply for transportation, but in lesser scale. Yucca was not as dry or geological stable as initially thought, and the requirements for "permanent" disposal are very stringent, so Yucca is not considered anymore for long-term storage.
I think the closer comparison would not be Yucca Mountain so much as deep bore hole research. You could essentially use the same equipment for boring your reactor hole to create disposal pits.
Maybe a breeder reactor would still be built to burn all this "waste" which is 90% fuel. Nuclear fission energy can become way cleaner when the political logjam around extracting and burning plutonium is unclogged.
