The game was originally going to have a much more dramatic, serious, and cinematic story than the simple one it has in the final game which would have also featured much more characters from the Transformers: Armada TV Show and toyline. Even show-exclusive human characters Rad, Carlos, and Alexis were going to appear in the storyline as well more Transformers on either side, different locations and wildly different scenarios among other things. This can all be seen hidden in a lengthy script in the game's data by a programmer who kept it in "for memory's sake".

The game went through a number of early titles throughout development including "Transformers Armada" (which was the name shipped with review copies of the game), "Transformers Armada: The Battle for Energon" and "Transformers Armada: Prelude to Energon", all of which bear the name of the show and toy line that it's based upon. However, when the game was launched at retail, the name was changed to just "Transformers" for unknown reasons.

There are cut Transmission logs in the game's data that took the form of Autobots frantically and intensely contacting Optimus and the crew from Iacon on Cybertron about the planet Junkion, a key planet from Transformers lore that contains a robotic race of technologically-adept robots. These logs would have featured Autobot characters not in the final game at all, including Scavenger, Jetfire, Smokescreen, Sideswipe, and Blurr. Another thing about the logs is that they also would have revealed the origin of the Decepticlones: Megatron took advantage of the Junkion's inventive prowess and their "Hyper Power" cloning technology to make his near unstoppable army. Spoiler:The off-world Autobots would have also warned Optimus and the Earth team about Unicron's arrival to Cybertron when the Earth team arrived at Pacific Island.

There are a total of 21 unused Mini-Cons in the game's data, some of which appear as text strings while the rest appear to resemble JSON files. However, two were extensively worked on before being scrapped. The first one was called "Endgame" and would have summoned large "holes in the fabric of space" that would have sucked enemies and objects into them. The second dropped Mini-Con is called "Bug-Out" and would have called upon "Emergency Warp Gates". Although Endgame was scrapped, his model was reused for in-game Mini-Cons Discord, Twister, and Overwatch.

There is an unused Game Modes tab on the disc that comes with data suggesting that there were other game modes planned like "Boss Mode" and "Explore Mode", however no further data exists on these modes.

A special PlayStation Portable port of the game was planned called "Transformers: 2nd Strike", but was cancelled by Atari due to the Transformers video game publishing license being given to Activision by Hasbro after the Transformers live-action film was announced.

Cyclonus' signature Mini-Con Crumplezone appears attached to Cyclonus' Vehicle Mode as his cockpit, but in Robot mode, instead of appearing alongside Cyclonus or part of his "chest", he instead appears attached to his left arm. It's possible this was done by the developers to make the Decepticon a little more intimidating during his boss battle.

The internal name for the Alaska level on the game disc is "05_GREENLAND". this suggests that the level was originally going to be themed around and take place in the Dutch-owned island of Greenland instead of the U.S. state of Alaska.

Also, internal file names for the Pacific Island level ("07_EASTERISLAND") reveal that it was possibly supposed to be Easter Island (Rapa Nui).