While creating modded Fusion.exe's for playing these Chaotix protos, I got distracted with 1229 and played it some. Notable differences after I played Isolated Island and Amazing Arena act 1:
Espio appears outta nowhere, Metal Sonic comes in from the front of the screen, and sits in front of Espio. If you try to touch him, he moves back. He eventually flies away, and the screen shifts to the right. Eventually, theres a purple flash, and you're in a different area in IIZ (there's no training zone in this proto, thank god).
This platform is not solid and bounces up and down when Espio tries to stand on it. Also, to climb walls with Knuckles, you must hold the jump button, otherwise he jump off the wall (much like Vector in the Final). Also his climbing sprites are different. The level is only one "part" long (there's just morning), and the layout is different.
Different end signpost.
Different Special Stage art. IIRC this was seen in early magazine shots. I quite like it.
Holy Ring? What were they thinking?
Newtrogic High is mostly intact, however the Combi Catcher is not yet working. Instead, the makeshift NPC SELECT screen from Time Attack mode is used after your level is chosen.
The light switch is not present in Amazing Arena, nor is the mini-boss. However, you can complete the level regardless.
When you call your partner, your sprite is in front of their's. Heavy looks so much smaller by comparison. =P
Special Stage 2. This one is a lot uglier than the first one.
And after that I got back to work, so that's all I came across.