I would ask whether those differences are from the language or the framework. I won't dispute that Microsoft produced frameworks that are better than a lot of the frameworks you find in the Java world. But the little bit of experience I have says that Java coded in a sane manner performs very well and has good memory usage properties. Not that I've looked, but I haven't seen anything indicating major difference between the raw performance of .NET and the JVM. And I know the JVM today is much, much better than it used to be.
Speaking personally when I'm forced away from Perl I'd prefer to go to Java than .NET. But that is due to disliking Microsoft, and not wanting to have any factor locking me in to any Microsoft platform.