According to Ethan Einhorn, the producer for the collection, the three "lock-on" games (Knuckles in Sonic 2, Sonic 3 & Knuckles, and Blue Sphere) were not included citing "tight development times", and that including them would have meant "dropping several titles from the collection altogether", specifically the aforementioned nine unlockable games since "they all required unique emulation solutions".
Sega Mega Drive Vinyl is a soundtrack featuring music from the games in this compilation and was only made available in Australia and New Zealand. The release was limited to 3500 numbered copies worldwide.
The compilation received mostly positive reviews. IGN gave Sonic's Ultimate Genesis Collection a 9.0/10 score and an Editor's Choice Award, praising the addition of a rating system for each game and the Streets of Rage series, among other things. Greg Miller of IGN said that he "can't recommend this game enough".Retro Gamer rated the game 98%. It also received the award for Best Anthology in GameShark's Game of the Year Awards 2009.