Honestly, it appears the attraction for the 88mm and the 94mm is that they are proven calibers in the real world that worked(for the most part). Really, penetration, velocity, and max ceiling the shell achieves depends more on the gun and the shell itself, not what caliber it has; the only real difference caliber has is that larger caliber shells are heavier(
Duh). Basically, we can design a gun with a shell in any caliber we want and it will(probably) work as long as we specify what it is for(howitzer, AT gun, AA gun, general-purpose).
However, many people object to breaking the 40-80-160-320 progression we have going, and that's what's causing most of the flame wars. Though, we'll probably have to get at least SOME intermediate calibers, if only to get some good naval guns that combine the good things about the 80mm(lighter weight, good rate of fire) and the 160mm(heavy punch, very good HE shell).
One thing is that when it comes down to it, the thing that really matters is balancing muzzle velocity with shell weight to come to a good penetration number. For example, two guns have roughly equal muzzle velocity. One is a 40mm while one is an 80mm. It's true that the 80mm shell would hit with much more force(being twice as big as the 40mm(and thus due to the square cube law, being 4x as heavy) while still traveling at the same speed), the 80mm would require a proportionally larger powder charge(and thus a much longer and heavier shell) , which WILL reducing reload times as crews need to wrestle a more awkward shell into place.