Most systematists today would argue that morphology and molecules, on average, are equally likely to yield a significant phylogenetic signal. That's just with modern bone tests. Agreed, this can be a problem - but missing data can be a problem with the living, too. A good question. And it makes a great case for more field work.
Soft tissue can be as informative as hard.
We paleontologists rely on bones, of course, but that's our problem.