I enjoyed reading this article and felt that it identified many important issues facing an IT department when choosing an enterprise solution.
It would be revealing to port the Pet Store demo application onto one hardware configuration using both .NET and J2EE, with or without tuning, and then compare the results. Extending the test onto multiple hardware configurations would also clarify the issues.
I respect and understand the business forces bringing .NET to market quickly but when it comes to mission-critical applications platform maturity and a long-established track record are huge factors in any IT decision. This "first-cut" at comparing .NET to J2EE using a flawed apples-to-oranges comparison does little to convince me .NET is much of a threat to J2EE. Furthermore I would like to point out that J2EE enjoys a developmental lead--going back to the platform maturity issue.
My opinion concerning this "Cat Fight"? .NET is the underdog, J2EE is the established leader.