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The star/flag pole thing is misdirection. This is what is actually different about 2D versus 3D Mario:

In 3D Mario - especially with all of Galaxy's refinements - the path to the goal involves solving many physical puzzles and using Mario power-ups as tools required to navigate scenarios designed around the use of those power-ups and gadgets.

In 2D Mario, the entire course to the goal can be navigated with multiple strategies. The player can make it to the end as Tiny Mario if he chooses (or is forced to). Power-ups become tools that change how the player can attack the level. Because of this, there are different levels of skill that can be displayed - players can invent many strategies. Stark runs as tiny Mario, fireball runs, helicopter suit (in NSMBWii), riding Yoshi, etc etc.

3D Mario is designed as it is "because it's there". It's inviting to use the 3D space and mechanics to invent complex platforming and a variety of puzzles, and to create power-ups and tools that are worked into the level in ways that are more complex than 2D Mario.

The comparison is to look at the transformation blocks in Yoshi's Island. These are not regular power-ups. They're puzzle components that exist only to be used in specific places. This is what the power-ups / gadgets in 3D Mario are like. And because of this, Yoshi's Island is somewhat more limited in how it can be played than 2D Mario. There is one "optimal" way to play through a stage. (Yoshi however, adds replayability due to its scoring and collectable system that grades players on how well they did in the stage.)

This remains the biggest flaw of 3D Mario. The 2D games can be replayed with more of a hook - "what can I do this time? What do I feel like trying today?"