PageRank has nothing to do with h-index to my knowledge. The problem with using PageRank-like methods for academic papers is that academic papers mostly reference backwards in time (except for the occasional draft or work-in-progress being referenced, but proper cycles are rare). A triangular matrix doesn't yield an interesting stationary distribution...
I don't know if it makes any difference, but if PageRank should replace the h-index, the most direct equivalent would be to rank the authors rather than the papers, no?