Skip the 6 hours to/from Berlin (leaving you too little time to do anything there) and do Warnemunde, Rostock and Schwerin. Alla and SPB both offer tours here and if combined with St. Petersburg, you get a discount.
For all stops in St. Petersburg, used SPB. Leba, our guide was the best guide we have had on a tour in a long time. She was so knowledgeably and even though we did a lot, we never felt rushed or short-changed. The small group made it so easy to both hear what she said AND to make some extra stops or extend things a bit on some things. And we just breezed by some of the large Princess tour groups.