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Botanic Base is the most complete stage in the 1207 prototype. It is just missing a few Badniks and some polish.
The background pillar-like structures with waterfalls are nowhere to be seen in the 1207 prototype.
Characters are not automatically centered when riding a lift, and the idle animation won't be prevented. There are also no sound effects.
You can also jump on top of lifts and get stuck. In the final game, the tops are not solid.
Blue platforms exist in levels 3 and 5, which repeatedly explode using the game's particle effects, only to reappear a second later. They are solid for the brief period of time between explosions, generating more blue particles while in this state. The object was removed from the final game.
Level 5
While the boss is somewhat functional, Eggman stops less often, forcing you to try and hit him as he circles the playfield. The bumper is also not spawned and the music stops when the battle begins. It is harder to control your character, as pressing or causes you to be pulled downwards.
If the player gets hit with rings, his/her trapped partner won't be released. This leads to situations where you can be hanging around in the "hit" animation.
There is no fanfare for beating the boss. You're just returned to the World Entrance.
Maps
References