Seeing as how SPM is roughly three-fourths platformer, turn-based battles have been completely scrapped. You'll now defeat your enemies the same way you would in an old-school Mario game. Usually this can be accomplished by simply jumping on the enemy's head. Every bad guy kill results in an award of coins, as well as points. Every time you reach a certain amount of points you'll gain a level, which results in an HP or attack increase alternately.

As your quest progresses, you'll be able to take control of additional characters, including Princess Peach and Bowser. Each character comes with a trademark special ability. Peach, for example, can temporarily float through the air using her parasol while Bowser can toast enemies with his fire breath. While SPM only lets you control one character at a time, you'll always be backed up by a Pixl (they're sort of a substitute for spells and second party members). You'll begin the game with a neon butterfly named Tippi, whom will almost never leave your side and acts as your characters' guide. As you unlock new stages, more Pixls will join you and lend you abilities from being able to pick up and hurl enemies to bomb-laying.
The most advertised feature of Super Paper Mario by far is the ability to switch from a 2D to 3D perspective. Wondering why this game looks flat even by Paper Mario standards? That's because switching to 3D transforms the entire area, allowing you to sidestep obstacles that were blocking your way in 2D. It also reveals enemies and items you couldn't see before. Switching from 2D to 3D is necessary to solve certain puzzles as well as reveal hidden areas. Beware, however, for remaining in 3D mode for too long will drain a special meter and cause you to lose one HP each time it depletes.

As Super Paper Mario was originally slated to be a GameCube title, it's unsurprising that the game makes little use of the Wiimote. Other than pointing it at part of the screen to reveal the occasional hidden door, you'll mostly be holding the controller horizontally and using it as you would with a last-gen game. This actually isn't a terrible thing considering full Wiimote function on a mostly 2D game would probably be a disaster.