I am going to have alternate stages in the next version, loaded by holding R+A (using Dantarion's ASL code.) Only certain stages (such as Skyworld for Brawl/P:M, Hyrule Castle for normal size/P:M size, and Great Bay for water/no water) will have alternates. The ones that don't will show this when you hold R+A:

This is to prevent the game from crashing while still making the filesize small.
The stages that will have alternates will have a plus sign in the lower-right corner - blue for a P:M-related alternate, red for others:


sounds promising

looking forward to the next release