According to the game's official website, over 100 characters were planned to appear in the game, yet only 70 are in the final product, suggesting that at least 30 were scrapped. Despite this, only eight of the scrapped characters have leftover files in the game, most notably including Faith Connors, the protagonist of Mirror's Edge, and Isaac Clark, the protagonist of Dead Space. Connors can be seen in the final game as a portrait on the second floor of Boudreaux Mansion, while pre-release press coverage for the game reported that a costume for Clark was planned to be obtained through a side mission later in the mansion, but was removed before release. Designer Brian Kaiser stated that while he couldn't remember the exact reason why they were considered, he believed their planned inclusion was mostly due to marketing. Despite this, they did have ideas for how they could be used in the game, such as having Faith be found on one of the roofs high up in the City, but this never went through. Aside from them, the other leftover character files are for Madison Gray (an original character who was planned to be the twin sister of Evelyn Gray), Odin Revolution, Ray, Sandra and Tad "Flipper" McCaffrey from the original MySims, and Proto-Makoto from MySims Kingdom (whose data suggests that she was planned to be a recruitable agent). Lord Daniel from MySims Kingdom was also planned to be playable at one point according to concept artist Genevieve Tsai, who drew a character icon for him, but was scrapped.

A sequel to MySims Agents called MySims Agents 2 was planned, but was ultimately shelved in Fall 2009. Years later on May 12, 2023, designer Brian Kaiser shared an old completed story outline for the game on his Twitter account. Based on the outline, the plot would have revolved around the player investigating a series of strange events involving an unknown energy source (later revealed to be seeping through portals from the Nightmare Realm), all while contending with the new S.P.A. director Morgan (a reworked version of the scrapped character Vice Admiral Morgan from MySims Kingdom) and her advisors Dragomir and Svetlana (reused from MySims SkyHeroes), who has shut down several branches of the agency as part of "restructuring" and captured Walker after he began to investigate them. Several characters from the original game would have returned, with Roxie Road, Jenny, Dr. F, Buddy, and Vic Vector all being part of the player's team as they solve cases all over the globe. While full gameplay details are unknown (aside from a new grapple hook mechanic), some pieces of concept art have been released since, such as designs for Morgan's various monster forms.

To avoid loading everything in memory when the player visits the HQ, recruitable agents are given separate archives for their models. Several Sims who are not recruitable have separately stored models in addition to their regular map models, suggesting they were intended to be recruitable at some point. The Sims in question are Chef Gino, Ol' Gabby, Barney Cull, Dr. F, DJ Candy, Alexa Lexington, Chaz McFreely, Chef Watanabe, Justice, Tim (whose files were used in an earlier build of the game), and Proto-Makoto (a character who was scrapped from the game entirely).

During the game, Dr. F will say "It's dangerous to go alone. Take this!" - a famous quote from The Legend of Zelda.