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A reality check... you have to live with both
The reality is that you have to use both environments. The secret is not the actual platform, but the quality of the architecture! The SOA (Service Oriented Architecture) is the way to think.
Of course, from real experiences, on multiple projects ranging in size from $50K and $30M; I would pick J2EE anytime. Again, based on past experiences, I have seen much greater rate of failure and unstability on the Microsoft platform.
Bottom line, be wise and don't discard either framework.
One final comment... the last line should have read:
"...but comes down to three: .NET-proprietary, J2EE-generic or J2EE-vendor specific..."
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