Hi Vladimir,
Thanks. Sorry I didn't update this page, but I had already found the solution to it along the same lines as your suggestion.
The first problem with JAX-RS was with the bundling of the JAX-RS 1.1 APIs but not from the Cloud SDK, but from our own app. I missed to see that it was one of the transitive dependencies for Jersey, and I was running the older version of the same (version1) which supported only JAX-RS 1.1. That along with CXF 3.0's JAX-RS 2.0 was creating the issues. That was resolved.
The second issue with Jersey annotation scanning, as you pointed out rightly is an OSGi container issue. Will take a look at Tomcat 7. But any estimation when Tomcat 7 would make it to production environment?
Once again, thanks 
Regards,
Bhuvan