Ultimately, even a points system is arbitrary. The best cure for this, is, of course to use historical match-ups. Date of introduction is a huge cure, as many of the more powerful ships were not in service until the war was well advanced.
The US navy is a pretty different animal in 1941 than she is in 1945. The Japanese Navy started the war as one of the most advanced and modern in the world. The Japanese "got" naval air power early. VaS downplays the importance of air power, of course, so this advantage is lessened.
In contrast, the british and the germans did not develop as dramitically, they sort of stay at 1941 levels throughout. The Italian navy and the french navies are actually quite modern, but do not get much credit, as they did not participate as heavily in the war.
The differences most people see, are of course in Battleships and battlecruisers. When you get into the level of cruisers and destroyers, you have realtive parity, for a variety of reasons. But fleet selection is left up to the players, and the US and Japanese have access to the dreaded Yamato and Iowa classes. Below these ships, there is again relative parity: the Kongo and Nagtos are not that much improved over the Hood or Bismark.
Of course, ultimately, a game is not decided in list building. This is a concept I can never successfuly convey to my WH40k playing freinds, who, when they lose, try to find ways in which my list is cheesy because my list beat them.
You don't lose to a list, and you don't win with one. You win or lose as a player. Know your ships, know what they can, and can't do, and know your objectives. Then play your game as best you can, and hope for the luck of the die.
Ultimately, in this game, a Yamato whose player rolls few hits is less dauntng than a queen elizabeth whose player is rolling fives and sixes. This sor of this is impossible to balance, and even a points system will not make it completely fair.
