i am trying to generate grid for turbulent flow in a converging duct with curved boundaries.i want to know Whether the alignment with the flow direction is more important or minimum skewness is more important? Because i felt one has to compromise on one of these things. Any suggestions....

As you point it out, you have to make compromises! First it is obvious that you will never align your flow and your grid if you're using a triangular/tetrahedral mesh. So assuming that you're using quad/hex mesh then you will be able to align flow and grid. This could result in a decrease of the numerical diffusion (i.e. numerical error) but in simple flows. According to me, as numerical diffusion is not that high in convection dominated flows, you should better consider minimum skewness as "important factor" and choose a 2nd order scheme to solve the flow .

Regards