The game was updated heavily from its original incarnation, as it was noticeably older than the last two ported Mario games. This version is taken largely from the Super Mario All-Stars SNES cart, which has highly improved graphics; extra polish has been given to this version, especially with sounds and music. Parallax scrolling in the backgrounds, a graphical capability that was used in the All-Stars version, was taken out of most levels of this version. The parallax scrolling is comparable to Super Mario World which only had 2 layers through every level. However, some may notice that the clouds in the background "overlap" the mountains when they fly up to the sky. This version also contains a rumble feature when used with the Game Boy Player on a GameCube.

This game also featured a save system. The save system was very controversial, as some players perceived it to be awkward and clunky. Defenders argue that the developers may have wanted to encourage some replay value, citing an interview with Takashi Tezuka regarding New Super Mario Bros.. In the interview, Takashi Tezuka says that you can only save from world to world(later changed to clearing each tower, similar to this game), saying that this encourages replay value. There were two types: temporary and permanent save spots. Players could make temporary save spots at any time; the save point would be erased when accessing the save, and the player would have to save again. If they forgot to save, the game would revert back to the last permanent save point. There are approximately 8 permanent save spots:

After beating each Koopaling (7)

After beating each Fortress (1)

After beating the tank levels in World 8 (0)

It is impossible to beat the first three items (Koopaling, Fortress, and Tank) again after beating the game, unless it has been defeated with a completion score of 100%. For this reason, the World 5 permanent save point is very popular to create a permanent save spot (to preserve the score and items box) after beating the game.

After fully beating the game (every level), temporary save spots are removed, and each save is now permanent (the player must still go back to the title screen, however). Players can also save on the map screen as well.

Super Mario Advance 4 was one of the few games to have a fully-fleshed e-Reader extension. There were level, power-up, and demo cards. The levels are accessible in the Level Card option in the opening menu. In the main game, the player can bring up a menu with two options: "Demo Card" and "Power-Up Card". In the e-Reader world, accessing the levels menu showed the option of "Level Card" to load more levels into the game.

The cards were released in three forms:

SMB3-e series

Wal-Mart cards

Special demo card included with the game

In Japan, two sets of cards were released; America also got two but they only had one-third of the number of cards that the Japanese sets had. There were 50 cards in Japanese series 1 & 2; the e-Reader was not released in Europe. They are the same size as ordinary playing cards and come in three types: Power-Up, Demo, and Level Cards.

When players wanted to play a demo, load a power-up, or load a level in, they would need an e-Reader, two GBAs, a link cable, and the appropriate card. The player would stick the purple connector into the GBA with the cart, and the gray connector into the GBA with the e-Reader. The player would turn both units on and load up the option to connect to the e-Reader in SMB3. When the connection was set, the player scanned the cards, and disconnected when finished. Because of the need of a link cable and another GBA, this function will not work with the Nintendo DS