Yuji Naka in the Sonic Jam Guidebook said:
At first this stage was set to appear about after Zone 10. Although there would be fewer Acts this time, we thought having about 18 zones would be good, but having each zone stand out and fit in the story in a way that was easy to follow, in the end it dropped down to 11 zones, and Chemical Plant was placed as the second stage. In the end, it was a success (laughs).
Chemical Plant, aside from the whole "megamack" sections, isn't a particularly hard zone, so it makes sense that it would be moved up. Just like the aforementioned Labyrinth Zone example, but in reverse. But really, Sonic the Hedgehog levels are about diversity. Even in Sonic 3 & Knuckles, which has the level transitions, you had levels that might not make exact sense in the order they were received if you weren't given an excuse for them. Jungle level, underwater city, ruins area, modern carnival, snow covered mountaintops, tropical shoreline built over with a launch base, mushroom covered forest, flying fortress, desert level, lava filled cavern, non lava cavern, floating ruins, flying fortress, and just space. Really, it's only the last few levels that actually flow into each other, just like in Sonic the Hedgehog 2. To be perfectly fair, that's all you need. I don't want to go through four tropical levels followed by four city levels. I want to see as much of Sonic's world as possible in one game, jumping from one location to another and not having any idea what to expect next. As long as it starts in some hilly landscape and ends at the heart of Eggman's latest base of operations, I could not care less what the order of everything is inbetween. As long as there is a gradual curve of difficulty.
Hell, you can even say the same thing about Sonic Adventure. The hubworlds are an excuse to get from place to place, but that doesn't always make the flow of levels make sense either. Emerald Coast, Windy Valley, Casinopolis, Ice Cap, Twinkle Park...not exactly a natural progression.
Maybe that is one of the things that bothers me about Sonic Adventure 2. They spent way too much time focusing on creating a flow of levels that actually led into each other. And that kinda hurt the game, because at the end of it, even if you had 30 separate levels, they were only in about four different locations. City, Desert, Space, Jungle. Nothing really special about any of them.