To open up V-Hard mode, go to One-Player Stadium and to the difficulty selection screen. There, hold the Z button, and press L, L, A, B.
To open up S-Hard mode, again go to the difficulty selection screen, but this time hold the Z button, and press R, L, A, B.
When you lose a match, and it asks if you want to continue, just press No. Then go back to 1P Stadium and continue your game. This way you start out where you left off, but it doesn't count as a continue on your Record.
At the “Puzzle Village” map screen, select the “Puzzle University” icon and select “Custom Puzzle”. Now, go and select your personal file and select any of the custom puzzles you’ve made. Select “Play” and beat it. Return back to the “Puzzle Village” map screen, and once again, select “Puzzle University”, select the original puzzle mode, go to the same personal file you selected for the custom puzzle and pick any class from 1 to 3 and choose any puzzle. When you check your puzzle play time it should be restarted by saying time: 00, 00 (or something like that).
Note: For this secret to work, you must have created a puzzle that is beatable.
At the title screen, hold Z and press B, A, L, L. You should hear a sound if entered correctly.
Start a 2 player game and at the ''Trainer Select'' screen hold Z + L + R on controller 1 and controller 2 at the same time.
To access the secret Mewtwo stage in Two-Player battle, go to the Select Trainer screen in 2-P Stadium. Now, hold the Z button, and press B, Up, L, B, A, Start, A, Up, R. You'll automatically be transported to Mewtwo's stage. Player one will always be Ash Ketchum and player two will be Mewtwo.