The new game builds on the innovative control system pioneered by its predecessor, with PES 2009 adding a wide range of new control and content elements which will affirm its title as the definitive football title for the Nintendo console.

PES 2009 for Wii boasts three control methods, with the intuitive 'point and drag' interface of last year's game enhanced to make defending and shooting more instinctive. Players use the Nunchuck or the Wii Remote to control the player on the ball, while they pick the player to pass to, or send them on runs into space. The system has been further refined, so that close control is improved, but two new control ideas have also been implemented.

Users can now play PES 2009 using either the Classic Controller or the Wii Remote held sideways. Selecting these offers a take on the classic PES controls from other versions, with the many through balls, chips and shots allocated individual buttons on both controllers. Mixtures of these systems can also be allowed during co-op multi-player games, with users opting to use their favored system from the user-friendly menu system.

Other key advances include the addition of the UEFA Champions League, the greatest club competition in European football, as a stand-alone option with all-new introductory elements, and a greatly expanded Champions Road mode. Champions Road is an incentive-based game, wherein players are rewarded for success in competitions.

Players are given individual challenges, each of which is allocated a cash bonus. These range from scoring a hat-trick, to string multiple passes together, etc, and the monies raised can be invested in improving the facilities at the user's chosen club. Everything from oxygen capsules through to private jets can be bought, all of which will help entice better players to the club, while the players involved improve their experience stats during matches.

The Wii game also marks the introduction of the Master League, which has proven so popular in PES for other home gaming formats. Master League places the player in charge of a lowly team and charges them with building their reputation and success through astute signings, good on-field performances and training methods. Every aspect of overseeing a club falls under the user's jurisdiction, with success on field used to attract new talent and build a team of stars capable of succeeding in PES 2009's many cup and league competitions.

PES 2009 also has a greatly improved online mode, with up to eight players competing online at once, using two consoles and with four players per Wii console.

Anything up to four against four is allowed online, while offline allows for four players simultaneously. Players can also now use their Mii avatar within PES 2009's Match Mode, and within Champions Road. Miis are easily assigned in both sections, and can also be used within co-op matches.