Sonic the Hedgehog 2 is rather famous for the number of Zones that were planned for inclusion but ultimately cancelled, particularly the Hidden Palace Zone, of which there are traces scattered throughout the final version.
A new HPZ loosely based on the original level using the same graphics and enemies but with different layout and gimmicks and stripped off its BGM, lore and intended functions was much later implemented in in the 2013 iOS port, courtesy ofPromoted Fanboys.
Prior to the iOS Sonic 2 port, the stage had been revived as the Zone of the same name in Sonic 3 & Knuckles with new graphics, BGM and layouts, but keeping the same concept.
One of the planned Sonic 2 Zones is still partially in the game. The third act of Metropolis Zone is a modified version of a scrapped one-act Zone called Genocide City Zone. Which would likely have been called "Cyber City Zone" in the final version (presumably after consulting with people with slightly better knowledge of English vocabulary), and been largely an Expy of the first game's Scrap Brain Zone; it's telling that Metropolis Zone Act 3 was actually included for the sake of using the map they designed for Cyber City Zone, lest they waste it.
It was revealed that Sonic 2 was originally meant to use time travel, but time constraints prevented this from coming into fruition. Sonic the Hedgehog CD ended up using the time travel idea.
On the topic of Sonic CD, there are quite a few sprites that were found in the beta version, but were left out in the final version. Some of these being: Sonic sneezing, turning black when being killed (perhaps as a result of being burnt?), hung from something, electrocuted, etc. You can see those as well as several others here. And then the 2011 Enhanced Port was set to have two bonus levels called Desert Dazzle and Final Fever, but they got the axe because Sega didn't want to stray too far away from the original game.
There was also going to be a fan made HD remake of the game with every sprite redrawn to have very high quality. The game was released in its alpha state, though only the first zone was playable. There was more planned, but due to infighting between the developers, the project never progressed and it was eventually canned. However, in mid-2014, some of the team got back together and is planning to rebuild it from scratch.
Less well-known is that Knuckles Chaotix was seemingly planned to feature several more characters, including Sonic. Also, the game was based off a cancelled game called Sonic Crackers, which went by the same concept, except with Sonic and Tails.
Also, Sonic X-treme was originally going to be a 32X game codenamed "Sonic Mars", and was going to be based off SatAM.
In fact, Sonic X-treme had a very complicated history before they settled on the Saturn incarnation. And does anyone remember Chris Senn's Project-S? Unofficial though it may be, it would have been the closest we'd see of a complete creator-designed X-treme. Alas, the project was never completed, but in late 2013, a new game called Sonic Lost World will be released for the Wii U and 3DS, and it's the closest to X-treme we will ever get.
Sonic the Hedgehog (2006) is no doubt a rushed, unfinished game, but this is only made worse by the fact that it looked promising at one point. Early tech demos from 2005 promised an actively changing day/night feature, an advanced physics engine, and a "free play" mode allowing players to control any of the characters, unbound by storyline. What we got is clearly a different story, but there are still remnants of the good ideas that once were: Crisis City is a graphically impressive level, for example, and if one digs around in the code of the game enough, the developers wanted to include Super Sonic as a playable character. Here's an example of an early trailer for '06
Also uncovered in the data was evidence that Metal Sonic was going to be given his own part in the game, such as missions, and even a story.
Originally, Silver was going to have a purchasable 'Light Chip' item that would allow him to run the same speed as Sonic and Shadow. But due to the game being rushed out the door before being completed, the powerup was left out and he remained slow.
Early versions of Sonic Adventure 2 supposedly only had Sonic, Knuckles, and Eggman as playable characters (Shadow and Rouge would have always figured into the plot). Fan demand caused Shadow and Rouge to be made playable, and Tails to join the roster. This is the reason why each new addition is an Expy of one of the three existing characters. They receive a slightly lower amount of stages than the first three, most of which reuse locales and objects from levels meant for the original three characters.note Tails and Rouge each have four levels using their "normal" gameplay, plus a driving stage. Shadow only has four levels period, the least out of anyone. He also doesn't participate in the true final stage, Cannon's Core, but the reason for that is plot-relevant. There was also to be a branching storyline affected by the player's decisions; an idea revisited in Shadow the Hedgehog.
There's even more to the development than that. Rumors have it that Sonic Adventure 2 was going to have Adventure Fields akin to Adventure 1, and early concept artwork of Shadow involved him with amputated limbs, missing eyes and he may have been the original final boss, instead of BioLizard.
The original concept for the series was considerably different. Originally, the concept for the game while Sega was coming up with a new mascot to rival Mario was a speedy rabbit that grabbed objects with its ears. This idea was tossed because the team felt that such a mechanic would slow down the pacing of the game. The game Ristar revived the concept and is basically how the gameplay for that game would have been (only slower-paced and with the character being a star that grabbed stuff with his hands rather than a rabbit using his ears). It's also noted that Sonic was chosen over an armadillo◊. When it was narrowed down between just these two designs, Sonic was chosen due to his spikey look.
There are sketches of Sonic with a blonde bombshell by the name of Madonna. It's said that she was supposed to have been Sonic's girlfriend, probably done to rival Princess Peach. Also, Sonic had several early designs; most notably, a Theodore Roosevelt lookalike in pyjamas (who evolved into Eggman), a wolf wearing an American flag t-shirt, and a bulldog in a cool outfit. Interestingly, both of the latter were Fully Dressed Cartoon Animals. See them for yourself here.
Speaking of Sonic Adventure, after the cancellation of Sonic X-treme, Sonic Adventure was announced as a Saturn game, and according to a prototype video, it was going to use the same 3D models from Sonic R.
The "Sonic World" hub in Sonic Jam was actually Sonic Adventure's engine test. Once production switched from the Saturn to the Dreamcast, Sonic Team touched it up a little and added it to Sonic Jam as an extra.
There was originally a robotic dragon Sonic and Tails had to face in one of their flight stages. The data is still there and, when hacked back in, reveals that it would have been in the first flight stage.
Sonic the Hedgehog Spinball had its own version of the early Sonic theme before the switch with Sonic 3. However, the music development team found out that Mastao Nakamura had owned the rights and not Sega as they assumed. Howard Drossin quickly whipped up a new jingle.
A Prototype shows possible cut scenes or at least stills of Eggman viewing Sonic's progress through the Veg-O Fortress. The Machine stage also had a different tune.
When Sega held auditions to replace the 4Kids cast in 2010, Ryan Drummond was contacted to re-audition for the role of Sonic. However, because of Drummond's union status and his refusal to quit it, he was eventually declined the role. While Roger Craig Smith certainly isn't doing a bad job, many fans would've loved it if Drummond voiced the blue blur again.
Similar to the Luigi's Mansion example below, Shadow the Hedgehog was going to be the first Sonic game with a Teen rating. Originally, enemies were going to bleed red blood, and in the intro, Shadow's flashback to Maria's death was actually going to show her being shot on-screen. But the ESRB threatened Sega that they'd slap the game with a Teen rating if these were kept in... which you may end up finding weird given the game was actively advertised as more mature than predecessors. What happened? Turns out ESRB introduced "Everyone 10+" rating in the meanwhile, and Sega of America decided to go with that. So the blood had to be changed to green, and the Maria flashback ends as we hear the gunshot.
The blood and death scenes are still present in the Japanese version.
The game was meant to have used the voices of characters that had appeared up until Sonic Heroes. However, when Deem Bristow passed away during production, Sega hired Mike Pollock (Eggman's VA for Sonic X) before they decided to hire all of the Sonic X voice actors, whom stayed with the series until Sonic and the Black Knight. Except for Pollock, who's still Eggman.
In Sonic and Sega All-Stars Racing, Toejam And Earl were reportedly going to be included, but the developers could not obtain the license to the characters in time. Vyse was also considered, but the game was nearing deadline, so he was added into the roster in Transformed instead.
Sonic the Hedgehog 3 has an item monitor that can only be accessed through debug mode. The item in question is just a blue "S" that grants the character their super form and 50 rings, even if the player did not collect all the Chaos Emeralds. Whether the item was just for bug/balance testing or something more remains to be seen.
The magazine Sega Magazin makes mention of a "Help item". Sonic would break a monitor and whistle for Tails who would then carry him about akin to a second player. Although not present in the final game, Sonic's whistling animation is still present within the game's code and a whistling sound is heard at the start of Doomsday Zone.
Concerning Zones in Sonic 3 & Knuckles Flying Battery Zone was originally intended to be a level in between Carnival Night and Ice Cap (a different level select icon for Flying Battery Zone can be found in the game that suggests this further), originally the cinematic at the end of Flying Battery involved Sonic breaking out of the ship and using a sheet of metal from it to Snowboard down Ice cap much like he does with the random snowboard in the final version of the game. This was changed to give the Sonic & Knuckles half of the game more Zones that played more traditionally (not counting Hidden Palace and Doomsday Zone which don't play like traditional Zones) so it wouldn't feel shorter than the Sonic 3 half, though this concept was re-used as the inspiration for Sonic Adventure 2's Hero Side opening cinematic and the start of the City Escape level a couple years later.
One piece of music, "Open Your Heart" by Crush40 (their first song, actually), was not written with a video game in mind, though at least composer/guitarist Jun Senoue was working on the game already. In contrast, "Who I Am" by Magna Fi was intended for Shadow the Hedgehog alongside "All Hail Shadow," though Executive Meddling from the band's record company resulted in only the former being used that way while the latter eventually ended up as the first song on their final album, VerseChrousKillMe. (Seriously, hearing it with Shadow in mindnote especially the lyrics "This is who I am, not a shadow of who I want to be." is hard to unhear.)
The Christian Whitehead-spearheaded iOS remakes of Sonic CD and Sonic the Hedgehog 2 had Boss Rush stages planned out, with 2's Boss Rush stage using graphics from the canned Sonic Crackers demo. Though they're still in the game, they had been Dummied Out as Sega felt that altering the game too much would be majorly problematic.
Players also discovered what was called "Proto Palace Zone", a recreation of the original Hidden Palace Zone. Christian Whitehead confirmed it was just to test things out.
Simon "Stealth" Thomley developed a a proof-of-concept of the classic Sonic trilogy for the Nintendo DS when he heard leaked news regarding a Compilation Re-release called Sonic Classic Collection (which was developed by The Creative Assembly). All of the games were recoded for the DS, and included the following extra features: Tails and Knuckles were added to the original Sonic the Hedgehog, the elemental shields from Sonic the Hedgehog 3 could be used in the first two games, and Sonic 3's Special Stages had a Level Editor that included two new spheres — green ones that turn blue when touched, and pink ones that act as teleporters to another random pink sphere. Later in development, Stealth even wanted to include Sonic the Hedgehog Megamix in the collection, but he was unable to contact Sega during the first "Sonic Boom" event, and eventually realised that pitching Megamix as a commercial game was infeasible. Ultimately, Stealth was unable to make his take on the collection into a commercial game, but elements of it have since lived on in his collaboration with Christain Whitehead regarding the iOS versions of Sonic 1 and Sonic 2.