The Quantum Field space theme was remade in Backyard Baseball 2007 as Area 51.A Putt-Putt and Pep sticker and a Pajama Man comic from Pajama Sam can be seen in the background. The Baseball Darts minigame takes place inside the clubhouse from the SCUMM-era games.The GameCube version of the game features Barry Bonds, but it lacks Alfonso Soriano. The roster of MLB pros differs slightly between each release.This has caused one inconsistency: Achmed Khan says his signature pitch is the 'Zig-Zag', which is not featured in the game. The players' dialogue from Baseball 2003 were re-dubbed by new voice actors in Luanne Lui's case, her dialogue was rewritten to remove references to her teddy bear for good.The players' descriptions were taken from Backyard Baseball 2001 & 2003.Starting with this game, the slowball, left hook, and right hook pitches were renamed change-up, screwball, and curveball, which is the standard baseball terminology.

The themes in the GameCube version were the old themes.

Oddly, Sidney Webber uses Ashley's old theme for her walk-up music, but Ashley uses her new theme for her walk-up.

Vicki Kawaguchi's walk-up music is the tail end of her old theme song, and the Starlite Orchards Drive-In field uses Angela Delvecchio's old theme for its intro music.

The Doghouse NYC now provides the game's music. This is the first game where every pro has their own theme song.

Except for Pablo Sanchez, all the MLB pros and Backyard Kids have new theme songs.

In this game, longtime color commentator Vinnie The Gooch is replaced with Abner Dubbleplay.

Pete ran so fast however, he ran through the fence. Several accidents by the opposing team lead to Pete scoring an in-the-park home run. Angela Delvecchio accidentally throws a wild pitch, which is hit by Pete Wheeler while he was in the On-Deck circle. The intro video features several backyard kids playing a baseball game. Also new are two minigames: Fielder's Challenge and Baseball Darts. Clanky as a playable character in this game, he can be drafted in a season. Completing Clanky's Coaching Box unlocks Mr. New to the series is Clanky's Coaching Box, a tutorial on fielding. The ability to view the opposing team's stats during the game has been removed.

It is now possible to create more than one custom player for a team. Custom players can earn additional skill points by accomplishing certain tasks (such as hitting three home runs in one game). The Custom Player option is also expanded upon in this game.

Players can now get power-ups for pitching hitless innings and making diving catches. Leading off and picking off are now allowed. As this is the first 3D Backyard Baseball game, there are several gameplay changes.

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