Any article that includes the phrase "before I start a flame war" is invariably going to do just that. But Eberhard manages to tackle the 'Spring vs. Java EE' debate in as delicate a manner as possible, even going so far as to assert "I think "Spring vs. Java EE" is the wrong question." Is Spring solving all of your batching problems? Is Java EE helping you with cache performance problems? Probably not, so to assert that any framework is a modern panacea is just foolish.
On a related note, RedHat is running a webcast today entitled Java EE 6 and CDI: Moving away from the clutter of Spring and other frameworks. This webcast just might be a little less even-handed than Eberhard's editorial piece.