We're seriously considering doing the ports more or less on our own, with the obvious exception of St. Petersburg. Everything I read suggests that it's easy to get around in all of the cities, and I think we've decided not to go to Berlin. That way, we can save a fair bit of money and be ready to splurge in St. Petersburg.
We are also definitely leaning towards hiring a private tour guide for our family in St. Petersburg. It's probably more money than doing a combination of Disney tours, but I don't think it's a lot more money, and this way we can see exactly what we want to see, for as long as we want to (for example, I know my DDs are going to be good at The Hermitage for two hours max). We're considering a white nights tour which goes out at about 11 pm (the downside to that is how tired we will be the next day). We've emailed three private tour companies this weekend and have heard back from two already. They are all so highly recommended that I think it's just a question of which personality suits us best, as much as that can be guessed from email exchanges.