Starting stages:
Battlefield
Final Destination
Smashville
Yoshi's Island
Lylat Cruise
Castle Siege
Delfino
Halberd
PK Stadium 1
If thought about as a set unit along with the striking system, neither person should end up on a stage they don't want to be on. Just strike the 4 you don't want to go to... your opponent does the same. We don't want the match of Toon Link vs Ganon on FD. No person should be forced into a counterpick worthy situation on their initial match(the supposedly fair one). Characters that need to use "autocancelled" moves like ganon's dair can strike things like yoshi island and Lylat Cruise. Against Dedede and others that can chain grab effectively, striking Castle Siege and Delfino would be an option. The transforming stages have quite a bit of balance to them however. Even Dedede is disadvantaged if he ever needs to use his upb on the wide island water situations... he also doesn't have a spike to take advantage of the water, while being a large target himself. The stages that you can go up through also add something to the neutral list that wasn't there before, and don't allow stage spiking. Allowing for the 4 extra stages that weren't thought of as neutrals before adds options and strategy for striking. But nobody HAS to play on them, you only play them when you think they offer no effect on the match.
If just the original 5 neutrals (one that includes Lylat) were used, "autocancelling"-heavy characters would forced between striking against spam or against their move set. Overall, the 9 add a more balanced picking procedure for more characters and stray from a counterpick first match just a bit farther.
Counter List: Leave all in Counter list, If any from the counter/ban list pick Onett.
Notes:
Jungle Japes: It does its job as a counterpick. Great for those with horizontal recoveries and projectiles. If on the left side of the stage falco's chain into spike could be disadvantageous.... but that would depend on character. You can also choose to go into the water as a transportation method if you are getting edgeguarded/hogged. The one ban you get after the first match could be used here if need be.
Pictochat: none of the hazards damage too much. The transitions add quite a bit of strategy including faster ways to kill/damage. None of them kill too low, though... so it isn't the same issue as say the cars on aero.
We aren't really here to ban things that are already on the confirmed counter list...