Perhaps it is the scope of the project. Java projects seem to be bigger than that of .NET. .NET tends to be internal apps while Java app could be like some sort of mother-ship type of application (or what people used to joke as the "Command Center" software) or huge integration project.

Having said that, I agree that Java ecosystem is more difficult to learn.

Many students during my college time prefer .NET because VS.NET Express makes a lot of things easier compare to Eclipse, Java, Ant, classpath, etc (forget Maven).