I was looking over the different courses for Sonic 2 and the beta, and I think that Sega had some big plans for this sequel. (Even though most of them probably got scrapped due to time restraints and put into Sonic 3.)
Anyway, I think that Sonic 2 was originally planned to have time travel in a linear order. (Not like Sonic CD, where you could go to any time period while going through a given course. In other words, you beat the level, you see that same world in a different time period, probably the past, in the second Act.) These are a few examples. Just keep an open mind while you read them.
1. Green Hill and Neo Green Hill. Neo Green Hill (Aquatic Ruin) clearly has the qualities of the first Green Hill, but with an "ancient" theme.
2. Chemical Plant and Oil Ocean. One thing to note about those extremely gloomy Sonic cartoons is that Robotnik built tons of factories, ruining all evidence that nature once existed. This is Sonic's reality and his group of "freedom fighters" are trying desperately to kill Robotnik (A goal they never accomplish, if you think about it.) and destroy the countless factories he has made. The whole theme for the Sonic cartoons was "technology over nature" and what it leads to. Oil Ocean and Chemical Plant are definitely evidence that Robotnik ruined something important in the present. (It's important to note that the water in these two stages were replaced with Oil or Chemicals. Obviously, there were Oil and Chemical Spills that Robotnik doesn't address despite the damage to Sonic's world.) There's also the question of how this time traveling would even aid Sonic in the first place. Maybe Sonic learns about an ancient Chaos Emerald, (The one we find in the Hidden Palace.) and plans to find it and use it against Robotnik and his factories. (The little dino robots are evidence that it could take place in the past. But then again, they're still ROBOTS, aren't they?)
My head hurts. What does everyone think?