Scooby-Doo has many iterations, and every adaptation puts its own spin on things. According to Sarah Michelle Gellar, the 2002 film would have explored an attraction between Daphne and Velma (Linda Cardellini) had the studio not interfered.
Scooby-Doo is a simple formula: four teenagers explore haunted locations with their eponymous Great Dane, who serves as a mascot for their investigations. When it came time for a live-action adaptation, James Gunn was hired to bring Scooby-Doo to life. Originally intended as a more adult-minded spoof of the franchise, the film later underwent rewrites that brought a more family-friendly tone to the picture and cut out many of the nods and winks to the franchise's lore.
While appearing on Watch What Happens Live With Andy Cohen, Gellar talked about the deleted elements of the Scooby-Doo film. When asked about a rumored "side relationship" between Velma and Daphne that got cut from the final film, Gellar responded, "I don't know about a relationship on the side, but there was a steamy— I mean, I said it was steamy, but they probably didn't think it was, hence it was cut... Kiss, yup, it got cut. It was an actual kiss between Daphne and Velma that got cut. I feel like the world wants to see it, but I don't know where it is." Reportedly, the scene would have taken place when the Mystery Inc. gang was struggling to get their souls back in their own bodies, and the two would have kissed to return to their bodies.
Gellar also revealed a cut line of dialogue in which Daphne insinuates that Fred (Freddie Prinze Jr.), leader and planner of the group, was gay. The sequence was supposed to riff off of popular fan assumptions that Fred was gay or bi in the original iterations of the franchise. "There was a great line, too, where I'll never forget, we're having a fight, Daphne and Fred, and then I yell at him, 'And that ascot makes you look gay!' and I slam the door. They cut that too," Gellar said. "I think it was the reason I actually signed on to the movie. I know everyone's thought for a long time… there were always implications about Fred being interested in both parties. They all got cut. [The movie] was less family-friendly, to begin with."
This version of Scooby-Doo was intended to be watched by adults before it became a more standard family-friendly adaptation. To accomplish this, many sequences were cut, but these elements can still be felt in the final edit. Shaggy (Matthew Lillard) was intended to openly be a marijuana enthusiast in the film, a trait that's based on popular fan assumptions of the character. There are subtle jokes about this in the movie, such as Shaggy telling Mary Jane (Isla Fisher) that her name is among his favorites.
This version of Velma was also openly going to be a lesbian, but when the film came out, the idea was considered too "adult." Instead, Velma was given a male love interest in the second film, played by Seth Green. Nowadays, the idea isn't so far-fetched, especially since Velma has been depicted as bisexual in the Velma series, and the main version of the character is portrayed as being attracted to a woman in Trick or Treat Scooby-Doo!