Read Adam Bien's Future Of Enterprise Java ...Is Clear (Java EE with/without Spring and Vice Versa), including comments to get both sides of coin. I will choose Spring for several reasons and following is one of them (reproducing one of the comments from post)
'I am not sure which Java EE 6 server you are talking about. There is Glassfish certified and TMAX JEUS. It will take quite a while (read: years) until Java EE 6 compliant versions of WebSphere, WebLogic, JBoss etc are in production and can be used for real application. Spring 3 just needs Java 1.5 and J2EE 1.4 so can readily be used in almost all environments'