Question: I am quite aware of both java and C# .Net .when i try to create a new windows application which are the factors that decide which technology should be opted?
I know of one thing ,for great and faster UI development Visual studio helps a lot.

Answer: 
Choose the one with which you are most familiar. The two platforms are different enough that skills from one does not transfer easily to the other.

In any case, try making a trivial application in both your scenarios and see how it works for you. The initial impression is important as it is probably indicative of how well the rest of the work will be.
Yeah for a pure cross platform application Java can't be beat, but if you can manage it Silverlight is a subset of WPF and a pretty compelling cross-platform proposition on its own.

Productivity-wise I think WPF has an edge as it has a nice XAML markup language that can be easily created with the built-in designer in VS.NET or integrates nicely with MS' suite of expression products.