Talking to Himself: Quite literally with Classic and Modern Tails, who are both voiced by Kate Higgins. Averted in the Japanese version, where Classic Tails is voiced by Takuto Yoshinaga, while Ryo Hirohashi voices Modern Tails.
There was also a rumour of DLC stages being released. Apart from the Casino Night pinball minigame this was false (Though Sega did mention that they did consider making a DLC stage based on Wacky Workbench)
What Could Have Been: According to Word of God, they had hoped to make all acts playable by Classic and Modern Sonic alike. Indeed, it is possible to hack or glitch the game so that you can play Modern Sonic in Classic levels, viewed from a 3D perspective — the Classic levels look very unfinished when viewed in this way, however. The game reportedly crashes in various ways when attempting these hacks: e.g. when Classic Sonic triggers a rainbow loop, or when Modern Sonic doesn't stop after the Classic Finish Panel and falls through the level geometry... You can, at least, unlock the Modern Sonic homing attack, à-la-Sonic 4, for Classic Sonic, after collecting enough red rings in the Modern Era Act 1 levels...
Big's voice actor Kyle Hebert recorded lines of dialogue for Big's part of the game, but Big was later scrapped from the game's plot and levels. It's currently unknown where in the game he would've been, but Hebert's name remains in the credits, and Big's statue can be seen in the Statue Room.
Sega mentioned that they planned to make a stage based on Wacky Workbench, initially dropped to keep the "3 stages per era" set-up and later dropped fully when they decided against full DLC stages.
Some digging through the very first demo of the game (time-limited) reveals an option to change the HUD's appearance. This can now only be achieved through mods.
Originally the game was going to have three Sonics, with the third being "Dreamcast Sonic", who would have been voiced by Ryan Drummond. However, Ryan turned down the offer, so Dreamcast Sonic was scrapped and the final game had just Classic and Modern Sonic. Also, one of the staff at Sega of America did say that if Classic Sonic were to speak, he would have to be voiced by Jaleel White, but Jaleel was never approached about doing the role and they eventually decided to make Classic Sonic mute.
Cash Cash did the remix for the American Stardust Speedway theme for Generations, as noted in the liner notes for the remastered Sonic CD soundtrack, but decided against having in the game since Generations already had the "B" Mix remix they made and felt that the soundtrack should have something extra. This is also why the song loops on the soundtrack.
That's only going by the PS360/PC version of the game (Heroes is considered to be part of the Modern era in the 3DS version) and purely for pragmatic reasons (so that there'd be an even number of stages per era), though.
To clarify, while the PS 360 version of the game has Seaside Hill to represent Sonic Heroes, the 3DS version uses a boss instead, the Egg Emperor, that serves as a boss for the Modern Era, and all 7 of the game's Special Stages are directly taken from the Heroes style.
Word of Saint Paul: Ian Flynn, head writer of Archie Sonic comics, believes the Time Eater is what remains of Mephiles after the time reset from Sonic 2006. This is not confirmed nor denied by Sega.