There should be a standard, minimalistic way to bootstrap a CDI container outside of Java EE. This is useful for unit testing extensions, and for other JSRs that need to do annotation processing, injection and interception. Instead of those other JSRs defining their own mechanism for annotation processing, injection and interception they can just use CDI.
Also Java EE has clients (for JMS, RMI, Services). The same features on the serverside (injection, interceptions, proxying) are equally useful on the client side.
There should also be some clear walls between what is included in Java SE CDI and Java EE CDI. Java SE CDI being a subset and core of Java EE CDI. This modularity should be better defined in the specification.