i actually prefer bigger boxes. here is my reasoning behind it.
when i used to play guitar for a band called sirens,(now called a thieves parade)
i had about 9 pedals on stage. i used TWO breifcases that i coverted into pedal cases.
i had my overdrive, dirt, and chorus, oh and my memory man in one,
and in the other i had
my Dwarfcraft stomping double square snakes, ehx bassballs, dano sitar swami, and a bass flange in another case.
the bigger boxes helped to not accidently hit the wrong pedal and screw up a song.
plus you gotta figure, there are 3 foot switches on the E.C. thunder, so the more space between each one, the better.