I think strict31 has it right. Using a TREK example, many fans were impressed when TNG came out and we saw how HUGH the ENT-D was.
When the Romulan D'Deridex uncloaked and was even larger it had an effect on viers AND the crew of the ENT-D.
THe D'Deridex didn't HAVE to be built that big. It was done so for political reasons as well as tactical ones.
THe big battle/warship ship do have a few game advantages over the generally better crusiers and explorers, mostly due to being able to be a point or size or two larger:
1) THe slighter higher size means slighly more ability to soak damage (higher structure), that can be augmented by sacrficing SIZE for structure. Take a SIZE 8 CA design and change the size to 9 and call it a CB, DR, or BA and see what extra space you have left to "toughen it up".
2) That "extra" space in the larger ships can be reused for other things, allowing for some intersting refits. It is generally easier to squeeze on a few exra heavy weapons on a larger ship, since there is more "room" to play with. Squeezing and extra dozen phaser banks is easier on a bigger ship. Ditto with transporters, assault craft, whatever. This can lead to things like a Battleship being modified into a fairly decent carrier vessel. Just think what spending a couple of points of space on shuttlebays and transporters can do to of those big ROmulan Warbirds.