I would chose Java and not C# and not .NET and the main reason is that it is not clear if Microsoft will continue supporting them or switch completely in a java

I would chose Java and not C# and not .NET and the main reason is that it is not clear if Microsoft will continue supporting them or switch completely in a javascript/html5 environment. I would also question your willingness to write a desktop application because I get the notion you want to experiment rather than a real reason. In that case you can write your app in a non-web language and interact with it through other means.