In an interview at the 2011 Electronic Entertainment Expo with Takashi Iizuka, the head of Sonic Team, it was emphasized that the Nintendo 3DS version of Sonic Generations was specifically "a celebration of Sonic's portable history," with the more recent Game Boy Advance and Nintendo DS installments being an area of focus over the older Sega Game Gear titles. Despite this, the final game would predominantly feature content based on console games in the series. Out of the seven areas, the only ones based on handheld entries in the series are Water Palace Zone from Sonic Rush, and Act 1 of Tropical Resort, which is derived from the Nintendo DS version of Sonic Colors. All of the returning bosses are also pulled from console entries in the series.

In the original E3 demo for the 3DS version of Sonic Generations, the music used for the boss fight against Big Arms is a remix of the Doomsday Zone's theme from Sonic & Knuckles. This music is not present in the final game, with it instead being replaced by a remix of the final boss theme from both Sonic the Hedgehog 3 and it's said expansion.

Sonic Generations was originally planned to be released on the Wii, the PlayStation Portable, and the Nintendo DS. However, the only Nintendo or portable version that would see a release was the Nintendo 3DS version.

Due to its returning cameo in the background of Radical Highway on the 3DS version, NiGHTS is the only non-Sonic character to appear in Sonic Generations.