Well, it's been a few years and I don't know what's still offered, or your tastes, but I will offer a couple of personal opinions: If one of your stops is Warnemunde, many people take the train trip into Berlin. We didn't, but were told afterwards that it was stiflingly hot and that there were no refreshments or even water on board for purchase. We instead took a bus trip first to an amber museum, where I now wish I had bought a lot more than I did, and then to a count's hunting lodge which had been used as a hospital during WWII. Sounds dull, but it was a great trip. Our bus guide was extremely knowledgeable and answered a lot of questions about life in East Germany before and after the wall fell.
Also, in St. Petersburg everyone automatically goes to the Hermitage, and I guess it's a necessary-to-see-it thing, but in truth it is literally overwhelming. Room after room of paintings covering every inch of wall space, all the way up to the ceilings, with little or no organization. By contrast, Catherine's Palace was a delight.