I suspect that there might be inverse distribution of new and classic stages between systems, in regards to certain franchises. Compare the following:
Metroid = Pyrosphere VS Brinstar
Star Fox = Great Fox VS Corneria
Pikmin = Garden of Hope VS Distant Planet
Sonic = Windy Hill VS Green Hill Zone
Kirby = Halberd VS Dream Land (Gameboy Stage)
It seems that if a series gets a classic stage one system, it has a chance of getting an exclusive stage on the other. As a result, the Wii U stage roster could have something like this:
DK = DKCR stage VS Jungle Japes
F-Zero = Port Town Aero Dive VS SNES Mute City
Mother = Onett or New Pork VS Magicant
Yoshi = New stage? VS Yoshi's Island
Wario = New stage? VS WarioWare Inc.
This inverse-parallel principle doesn't seem to apply to the Big Ones (Mario, Zelda, Pokemon), nor to the "new" series (Animal Crossing, Kid Icarus, Fire Emblem, etc.). Some stages are shared, but I suppose that's only fair.
So my suspicion is that, in order to alleviate the stage workload, they adopted this tit-for-tat approach. Instead of creating 60- something unique stages from the ground-up, they used classic stages to lessen the workload across both systems (stage-sharing, like in Wily's Castle, would also help).
Basically, each system has 5 shared stages (e.g. Boxing Ring), 19 system-exclusive (i.e. "brand new") stages, and 10 classic stages (from Melee/Brawl). When I look at things in this way, the 3DS stage roster seems much more palatable.
You could take umbrage with how they only made 40 new stages instead of 68, but when you remember the immense workload (50 characters, two systems, modes, game balance, etc. etc.), it's understandable that compromises would need to be made.
EDIT: I hear that Pictochat may be a new Pictochat (i.e. "Pictochat 2"). If it is a new stage, then the cross-system distribution is 5-20-9; if it's the one from Brawl, the distribution is 5-19-10.