I went to Russia with my family in 2011 (for only two days!) and I would recommend the hermitage if the time of year you go isn't stifling hot - a large part of the hermitage has no air con.
I didn't see Russia by night - unfortunately we had to be back on the ship according to our visa but I would recommend seeing it in all manner possible. It's such a different place to go.
Apart from Moscow, I did the other included excursions with our guide and they were amazing - some of the best photos I have are from Russia.