Kaliningrad is an exclave and not connected to the rest of Russia. Good relations with Poland, Lithuania, and Belarus is the only thing thay allows goods to pass through Kaliningrad. Sevastopol is a superior port to Novorossisk for many reasons, but the biggest one is the crntral location in the Black Sea. The Black Sea Fleet can quickly deploy anywhere in the Black Sea from Sevastopol.

Vladivostok and the Kamchatka usually get iced in during the winter as arctic sea ice moves way down to the Japanese islands. Obviously that is becoming less and less of an issue, but that's why Russia claims the Kuril islands.