[quote=So Boerd]
Larger ships have a greater volume to surface area ratio. More space for shields and such. Sukui, how many of these things are coming at me?
[/quote]

But it also means more energy required to cover that ship in a shield. 

Though when it comes to maximum defense, you'll want maneuverability, armor, active protection systems (ECM) and hardkill measures, and supplementary defensive measures (such as shields, ablative armor plating or a superconductive shell for your ship; actively-cooled armor works too for lasers, though rolling your hull is a good tactic to employ when faced with DEWs). Making a giant ship that masses a lot decreases your maneuverability, and that's a bad thing when you're being attacked by projectiles coming at you at hypervelocity speeds. 

The only time I run with larger ships is merely to fill them with more missiles. But the Conjoining's proficiency with nuclear technology makes fielding large space battleships unnecessary.