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I understand about your confusion regarding Java and NetWeaver. It hasn't always been clear from SAP how much Java is involved in NetWeaver development compared with ABAP programming. Let's get your question sorted out, starting with the FICO side.
My feeling about breaking into SAP functional work is that if that's your goal, you should go ahead and pursue that directly from get get-go. There's a misconception that you can't break into SAP functional consulting without a "tour of duty" on the technical side. That's not the case.
On the other hand, there is another factor to consider besides which area you want to target: you also have to take your overall background into account. To get into SAP, you want to pursue the area of SAP that relates to your core expertise. In your case, since you are a J2EE developer, it makes more sense for you to pursue SAP technical careers. If you can find a role in SAP that plays to your strengths in Java, you'll have a better shot going after SAP openings than you would competing with functional consultants with deep SAP backgrounds.
Now, let's tackle the question of ABAP versus Java. Since the inception of NetWeaver, SAP has been back and forth on whether the NetWeaver emphasis is on ABAP or Java. At first, it was all about Java, but with SAP's customer base so heavily invested in ABAP, SAP realized that there needed to be a balance. Therefore, NetWeaver now supports both ABAP and Java development.
Having said that, certain aspects of NetWeaver development definitely favor the J2EE folks, such as Portals-related development work. The point is that a Java person like you would have a definite opportunity in NetWeaver environments. The best first step is probably to find any kind of Java work in an SAP environment. As you prove yourself, you should be able to move more aggressively towards NetWeaver-based Java work.
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