According to former SEGA employee Steven Frost, the reason why the game was panned by critics was because of "over-ambition" from the development team at SEGA:
"The biggest mistake in Boom was trying to cram too much into the game," he explained on SEGA Nerdcast. "Not only were we trying to make just a really good Sonic game, we were trying to add more to it. We overextended our grasp in some ways. We're trying to add in a bungee mechanic, and we're adding combat, and we're adding puzzles, vehicles, hopefully a more compelling story and a bunch of different environments. And it's just a lot, you know? If there's any lesson for me, it's that being too ambitious can be bad."
Rejected artwork exists for both Sonic and Eggman, showing potential redesign ideas that went unused.
During early development, the game was called "Sonic Synergy". This was revealed on the website of UX/UI design consultant for the game, Edward Moore. On this site, early design ideas for both Sonic and Amy were also shown, showing Sonic to be more similar in appearance to his classic appearance.
There is an early version of a cutscene still present on the disk, showing Sonic using a crystal shard.
Within the game's data are two unused voice clips of Amy saying "You go girl!" and "Way to go Perci". This may suggest that Perci was intended to be playable at one point during development.
At release a glitch could be exploited to give Knuckles infinite jumps in midair, allowing the game to be finished in less than an hour. This glitch was fixed in the January 2015 update.
According to an interview with Bob Rafei, CEO of Big Red Button Entertainment, the idea for the Enerbeam Tether came from Knuckles' Chaotix.