When it comes to battles, size matters. To balance that, Galactic Civilizations II introduces the logistics concept.
The logistics concept was designed to prevent the age-old strategy game issue where each side just builds a single mongo fleet/army/whatever and wipes out everything in its path. The number of ships you can put into a fleet is hence limited by your logistics ability which you can research to improve. How many logistics a ship uses is based on hull size.
In Galactic Civilizations II v1.0 that was:
Tiny: 2 points of logistics
Small: 3
Medium: 4
Cargo: 5
Large: 5
Huge: 6
It was done this way to keep it simple for players. But here's the problem -- ship sizes. A tiny hulled ship has 16 space. A large hull has 55 space. That's over 3X as much space but the large only uses up 2.5X in logistics. Advantage: Large hulled ships. There are other factors involved too such as hit points and cost -- which are well balanced. But logistics are out of whack in our view.
So in v1.1, it's going to be this:
Tiny: 2
Small: 3
Medium: 4
Cargo: 4
Large: 7
Huge: 9
The various logistics techs will be pumped up too. The fact is, we want people to be able to build swarms of ships as a viable strategy. We also want people to be able to fixate on building huge capital ships as well. Now, the current system isn't horribly imbalanced by any means, the guy researching the larger hulls isn't able to put in time researching some mongo weapons.
If you go strictly by a spreadsheet, you can see plenty of imbalances depending on how you want to look at it and how nit-picky you want to be.
But I want to stress - the guy who's building huge ships had to go and research (or trade some equally valuable) technology to those huge hulls. They also had to put together the manufacturing capacity to create them and make the sacrifice of putting their marbles into a single ship rather than a bunch. In addition, there are various "round off" things that they have to deal with as well and many components, particularly defenses, take size into account when determining how much size they use.
Update:
After play testing during the evening and taking more into account things like starbase bonuses and the cost of getting those large hulled ships I made a minor tweak:
Tiny: 2
Small: 3
Medium: 4
Cargo: 5
Large: 6
Huge: 8
The Cargo hulls didn't need to come down because the new logistics abilities increase your logistics quite a bit. Before you would have 12 logistics after researching enhanced logistics. Now you'd have 15. You could hence fit 3 transports into a fleet at that stage versus 2 previously.