Hi Pavan,
The main Two issues with the Wigner Ville distribution are :
Non-linearity of the Wigner Ville distribution and the presence of cross-terms also called as the "beats" in the literature. Although Wigner distribution provided a fascinating link between time and frequency domain in signal analysis, its interference terms are seen by many as unwanted artifacts. One big appalling reason for the use of Wigner distribution is that it can be computed very efficiently using the FFT algorithm.
There is a much more evolved framework for discretization - analysis and synthesis in wavelets, based on multirate filter banks. This is one of the major advantages that wavelets have got. I hope that this would resolve some of your doubts.
Thanks
TA