Putting jars inside the WEB-INF/lib is the old-style normal-java way of handling dependencies, and putting them outside the war is the new-style OSGi way of handling them.
By packaging your war's dependencies in WEB-INF/lib, you're treating them as normal jars (remember a bundle is also a jar). So in that case, you're right that there wasn't much point in using bundles.
One of the benefits of using wabs instead of wars is to get away from the dreaded 100 Mb monolithic war. Rather than packaging the bundles inside WEB-INF/lib, try having the war import the packages it needs using Import-Package:, and package the dependencies inside the eba. (If you don't remember to have the war import the packages it needs, you'll get the class not found exceptions you were seeing, because the OSGi container won't know your war needs those packages.)