It actually matters...
Less mass are the best option for getting the highest efficiency but you will get more expensive ships who are more difficult to upgrade.
Better quality is the middle of the road selection.
Reduced cost means you can get more ships out faster but your full fleets will be weaker.
They all have different results...
I like really tough fleets so I usually go with as much capacity and as much miniaturization as I can but those ships will be super expensive and filling up just one fleet take some serious dedication in shipyard production.
A human player in multi-player who choose lower cost ships could easily swarm my empire and destroy me if I have not pre-made a huge fleet. Lower cost make you far more dynamic and quicker to respond to losses, new technology or specially made ships to counter a specific enemy.