The game is largely similar to its predecessor, but adds some key features.
Several new gameplay features are introduced, including pre-match and in-match minigames. The pre-match mini-games are randomly chosen before every singles match, Test of strength, Stare down and Shoving match. Several in-game mini-games include the chop battle and a spanking mini-game for female wrestlers in bra and panties matches. The meter mechanic from the chop battles are retained, but the player must perfectly time the button press three consecutive times to win. If the player does so, a cut scene of the two female wrestlers kissing is played.
The ability to sustain a submission till the count of 5 once a rope break had been reached was also implemented. The game features several arenas that WWE held events at in 2003 and 2004; there are also arenas based on each WWE television show.
Also added to the game was the Clean/Dirty system, which influenced each wrestlers tactics. Players can choose if the wrestler is clean, dirty or neutral. A clean or dirty wrestler has a meter that can be filled up by performing special clean/dirty actions or moves.
WWE SmackDown! vs. Raw also includes a redone WWE PPV (Pay-Per-View) mode from its past games where the player can play sample PPVs from 2004, or create a PPV of their own by booking matches choosing match types and any superstar, legend or created superstar in the game. Created championships could be waged in the created PPVs. Before playing the PPV the game would show a generic highlight reel featuring two of the superstars in the main event of the show. Commentary began to improve and sync up with the matches more.
The game also featured an all-new Create-a-Championship mode where the player can create and defend the title in their created PPV. The game also includes the Create-A-Wrestler mode from previous games where the created superstars movesets, attributes, entrances, and brand could be customized. The create mode was improved from the previous game. Stables could be created featuring any wrestler game and entrances could be customized.
A new challenge mode provides gamers with opportunities to challenge themselves at different difficulty levels. In addition, several challenges put gamers in memorable matches from the past and beating these challenges will help unlock alternate attires and arenas.