here are a couple links I found on BEA's website --- hopefully they answer some of your questions:
Developing JSR 168 Portlets with WebLogic Portal 8.1 -- has a pros/cons table comparing BEA-specific portlets vs JSR-168 portlets.
Tech Talk: WebLogic Portal Server and JSR 168 this is a video interview, I haven't watched it yet, but it looks like it has potential.
Keep in mind that using non-JSR-168 portlets will lock you in to a particular vendor. If you use a JSR-168 compliant portlet -- then you can switch among the various portal-vendors.
Hope that helps.