We’ve thought of Omeka S and Omeka 2 as being distinct software, where the importer is meant to ease transitioning – if needed. Both Omeka S and Omeka 2 will continue to exist as parallel projects. Omeka S should not be thought of as Omeka 3, implying an upgrade path.
However, @Daniel_KM has produces a suite of plugins to make a more direct transition. That could be something to look in to for your needs.