Wow, I know distribution of Spartan Games product is slow, but I've never heard of that kind of problem.
Adding a Heavy Cruiser to a Cruiser Squadron can work very well. Because the Heavy Cruiser is slower and far less maneuverable, it plays more like a Heavy Cruiser Squadron as it moves across the table. The Heavy Cruiser gives the squadron more firepower and defenses, particularly Forward Fixed, Gunracks, Torpedoes, and Point Defense.
As for the Praetorian vs Naussica, both are solid Battleships. The Praetorian is a good, general-purpose ship, while the Naussica is all about offense. I find the Praetorian with 5 Interceptors forms a very solid position for the fleet to rally around, but I sometimes wish it had the Nausicaa's Mines and Forward-Fixed firepower.
For big games, take both!