The problem is people who would have the experience / knowledge to really make it better, are not tempted to go in and fix it, because there's so much political / non-technical work involved in doing that. If someone wants to solve hard computational problems, they might as well go into another field. If they really care about doing biology, chances have been that they aren't the greatest programmers (I understand this may be changing, but still seemed to be the case 4 years ago when I left bioinformatics). This leaves the people who are happy with the status quo, staying in bioinformatics, and the people who are dissatisfied, going to other fields where they feel their work can have more of an impact.
In my experience, what happens is that biologists define the science, and they depend on the computer scientists / engineers to implement solutions to their computational problems. The computational people depend on the biologists to validate whatever results they produce. The iteration cycle can be painfully slow, especially for people used to telling machines what they want them to do, and getting results immediately. The proposition of changing that dynamic is not alluring to most people, but I still hope there will be some who try.