There might be a need because I believe one input measure is missing: the quality of students. Many universities are "best students" attractors and this might be one main reason for their success. On one hand this is good, but on the other hand, between two universities with the same output I believe the one who takes on the worst students is doing a better job. So maybe we should be creative and figure out a way to take this into consideration.
But I must confess I don't believe much in rankings. Maybe we just need a new ranking if the (unnecessary) ones somebody invented are doing a bad job. I am not sure this is the case.