Well, Kunstkamera IS what is now the museum of enthnography (Peter's collection of oddities is the original core of the museum). I'd probably spend a bit more time there, but, on the bright side, it hasn't yet become a "must see" for cruise tours - hence no huge crowds and you can pretty much breeze through the exhibits.
Museum of political history is really good if you are into, hmm, political history and especially the history of the Bolshevik revolution.
Yusupov has a lot of history to it, but then it's just another palace, of which you will have seen enough by that point.
So, with those three, I'd subjectively rank them Kunstkamera, PoliHistory, Yusupov, but that's just me.
As a side suggestion - have you looked into Grand Maket? It's a bit less central than the other locations, but it would be an hour well spent.
Russian museum is also well worth a visit, and again, it's far less crowded than other attractions from the Top 20 list.