The first PES title on Wii was revolutionary in many ways. The new point and click control interface, only made possible by the unique nature of the Wii controllers offered a completely new way for players to interact with PES. One year on and the programmers have listened to feedback from gamers and made PES 2009 on Wii an even more impressive title.

The new game will retain the intuitive 'point and click' interface used to control both the player in possession of the ball and to send those around him on to runs into space. However, a new 'traditional' control system using either a Wii Remote or Classic Controller has also been implemented. Using a Wii Remote held sideways or a Classic Controller, the secondary player can control the game in a manner familiar to existing versions of PES for other formats. Thus, they can control using familiar PES controls while their co-op player orchestrates their player and the rest of the team using the bespoke Wii system.

An improved defense system will allow players to close down their opposition with more precision using the Z-Button, while a new targeting system sees the player steering where they place the ball when shooting. Coupled with better AI for the CPU-controlled players and opposition, the result is a more free-flowing and faster paced simulation. Set pieces have also been reworked, with more precision on free kicks and a wider range of corners than in the previous game.

In keeping with versions for other formats, PES 2009 for Wii will also feature the UEFA Champions League, the addition of the ever-popular Master League for the first time on this format plus the return of an enhanced Champions Road competition, an enhanced Edit Mode, more online gameplay possibilities, and a Mii Training sub-game system.