An unknown voice shouts "choose a player!" at the appearance of the character select screen.
A circular character select screen is shown, instead of Mario, Luigi, Peach, and Toad having to line up in a row.
A point system has been added. Players get more points for making one thrown object hit lots of enemies. If enough enemies are hit, an extra life will be awarded.
Hearts appear much more frequently than in the original. Whenever three or more vegetables or enemies are involved in a collision, a heart appears. Also, hearts can be pulled out of the ground.
Giant Vegetables have been added to the game. These voluminous vegetables take a long time to pull out of the ground, but function normally otherwise (apart from having a larger area to hit enemies with).
Giant Shy Guys and Giant Ninjis have also been added. These Shy Guys take a long time to pick up, and whenever they are thrown or involved in a collision, they yield a heart.
Giant POW Blocks have also been added. These bounce several times, each time having the effect of a normal block.
Shells were made larger, and they now bounce off walls and yield hearts whenever they collide with enemies. They also now take longer to pick up, and appeared in a little more levels. They can now hurt players, however.
The insides of vases were changed and so did the music inside the vases.
Starting the level, the player starts out with only one heart filled in the heart meter.
An extra mushroom was added per level.
In each level, there are five red Ace Coins. If all are collected, the player receives an extra life, and the level gets a star on it on the map screen.
When the game is finished, a new "Yoshi's Challenge" mode appears. Now, there are two eggs hidden in Subspace in each level, and the player must find and collect them all.
Mouser replaced Tryclyde as the boss of World 6. As a result, Triclyde only appears once in the game.
More enemies were added in the game.
Some things in the game, such as the Subcons, were completely changed in art.
Phantos now make noises when they move around the screen. Also, when the player throws the key down or loses a life, they exit the screen while moving forward, making them appear considerably larger than usual.
It is possible to remove Green and Red Birdo's Ribbon by jumping on him/her and picking it up, the player could either throw it away, or put it back on Birdo by throwing it back at him/her.
Clawgrip is now spelled correctly in the cast list; in previous versions, it was misspelled as "Clawglip". The Japanese release of this game, however, does not have the error corrected.
Luigi's overalls are now a similar color to Mario's, in the SNES remakes, they are purple.