Keep in mind that in the real world, there are considerations to be made other than "point cost" when it comes to designing, well, just about anything.
The key is in setting up the rules and norms for your campaign. Sure, mechanically, you can build a battleship that has the same acceleration as a fighter. But, in the real world, this would mean your battleship is 90% engine - "All legs."
So you set up the rules for acceleration by ship class, size, tonnage, whatever. Based on the rules and norms of things in your campaign - not the HERO Rules and Norms, but how you see things working, which you then translate into HERO System rules via campaign limits and such.