I still haven't got it to run for more than 10 seconds straight on Kega, but that's still enough to work up some differences. This is an image heavy post; however, all the screens are .png. So on with the list of differences:
As we all know, that awesome SEGA screen with the pic from the manual.
There's probably been some bitrot in this, as there's audible "beep" and scratch sounds throughout the music. This could also be a glitch, but I'm not entirely sure.
The title screen track has percussion thrown in, as well as most other tracks, as well as the aformentioned beep sound every ten seconds or so, in different variations depending on the track. Sometimes, those beeps seem like missing bits of sound that should be there, this is especially noticeable in
Amazing Arena. Probably bitrot wrecked these wonderful sound samples. Wonder why they took the percussion out, it sounds pretty nice.
All the Knuckles Ringstar malarkey, as well as Heavy being called Heaby in the title screens.
The backgrounds have scrolling issues, sometimes half the background lags behind, sometimes it doesn't.
Graphics flicker a fuckton, making the few bits of gameplay a hell of a lot harder to look at.
Marina Madness is unplayable, gameplay crashes upon touching the ground.
Training level shows Botanic Base title screen and plays the same music (Door Into Summer) that is found in the title screen.
Introduction level in stage select is vastly different from Introduction in "main" mode, at least from the few scroungable moments of gameplay, and plays the same track that the final does, however, in this beeping, percussion state.
World entrance shows no screen, has no collection minigame, no slider...You just run right through its emptyness and arrive at an NPC SELECT screen ( with the tiles shown in that one above post, in this case only including Heavy, Bomb, Vector, Charmy and a bunch of unselectable question marks), after which you will go to a level select screen, with vastly different names, the only one without a picture is "Amusement Park" or Speed Slider (screens below). However, getting these circumstances require SEVERAL emulator resets. All these weird zone select names are bullshit, however, since the title cards keep the final names. Also, notice how they spell "Atraction" with only one T.
All of the five levels are the same, however.
Two final enemies in Techno Tower (very basic routines, though), along with elevator:

This little green guy moves around for a bit and then stands still, expelling smoke.

This guy will go in a semi-oval motion above you and then leave the screen.
Pause move-around mode is always enabled.
Badnik in Marina Madness, resembling "Blinky" from Sonic 2:
Here's screens of the levels (At least, the best screenshots I can get):

Speed Slider

Botanic Base

Amazing Arena

Marina Madness
Well, this is about as much as I can find today, I'll see if I can get more stuff throughout the week.
Also, half of these screens are from sheer luck, especially the World Entrance ones.
EDIT: Yeah, I messed up on the names. Side-effects of sleepiness. Also, I haven't played Chaotix in AGES, my memory's a bit blurry. I'm pretty sure the orb and motobug were in final Chaotix now that I think about it, but could you get confirmation on the flying fish? And I'm pretty sure it's bitrot, the sound, apart from those missing beeps, has a "loud tape hiss" sound over the music.
If there's anything else wrong, go ahead and tell me, I'll fix it.
This post has been edited by Nabaztag: 24 February 2008 - 01:40 AM