Tikal mentions the ability to play Super Sonic in some Dummied Out sound files, complete with the original conditions.
Perfect Chaos looking the way he is in gameplay (an intangible light-blue dragon) is a result of graphical limitations at the time; He was originally supposed to look like the version from the intro (much darker, with more spines and scales, and opaque skin). Perfect Chaos would finally look like his appearance in the intro in the twentieth anniversary remake of the fight.
It would appear that early on in development, the characters (or at least Sonic) would've been in their pre-Adventure designs. If one looks closely in Sky Chase Act 2, Sonic's model resembles his classic design (though during the cutscene that plays halfway through it it switches to the model used everywhere else). Then there's this scrapped tutorial image from the Dreamcast version◊.
Turns out, said cutscene simply uses a low-poly model of Sonic/Tails, that is heavily based on their Sonic Jam models, but still includes the telling green eyes. Classic models from Sonic Jam are only seen in pre-release trailers.
A very early prototype of the game, called the "Auto Demo", has been unearthed and searched through. 3 test maps and many early maps were found, but the biggest find was the map geometry of the early Windy Hill, as seen in the game's earliest promotional materials. The map, along with structures in the test maps, suggested that the game would have been more dependent on Sonic's momentum, rather than his raw speed, and may have featured physics similar to the Genesis games.