I updated the OP and tested out most of these stages for Wii U counter picks. I haven't tested out Big Battlefield, Kongo Jungle, Castle Siege, or Duck Hunt yet. But I did test the rest.Mushroom Kingdom U, Pilot Wings, and Skyloft are banned.
Mushroom Kingdom U has the Nabbit stage hazard. If he didn't exist I would have considered this stage more.
pilot wings tilts like how lylat cruise does, but way worse to where it can actually harm gameplay. The plane can also collide with a cliff and kill a player randomly.
Lastly, Skyloft is out because there are some stage elements that can drag a player off screen unfairly with no way to get back to the stage.
There were also some changes in the additional rules regarding Bowser, Rosalina, Yoshi, Zero Suit Samus, and Peach that was removed due for the 1.0.4 patch.