JCZ: The original zone had a progression of starting out down on the coast and working your way up into the mountains. My pitch would be to reverse this, having Sonic and allies start elevated up on the mountains and work their way down to the sandy coast. Along the way, Sonic and the others traverse through various different small caves, many of which containing water in them which can generally be avoided with careful platforming. Characters such as Tails and Knuckles can take alternative routes that avoid the caves altogether.
TVZ: After thwarting Eggman on the beach, Sonic and the others find a valley not too far off that Eggman seems to have been dumping his waste into. For aesthetic and mood purposes, perhaps Act 1 could merely be cloudy overhead, though the sounds of thunder and lightning in the distance could warn of the impending storm. For Act 2, the storm begins, and the inclusion of rain causes some sections of the zone to become flooded, though as with the previous zone the player can avoid going in the water entirely. Powerful winds could also blow through some of the narrow sections of the valley in this act, pushing the player towards or away from progression. Players must avoid being pushed into harmful goop, while making use of bouncy goop occasionally to progress.
VFZ: Perhaps this zone could have a theme of darkness and light in addition to the whole mystical, mysterious thing it has going on. Sonic and the others must find their way through the mazelike forest, occasionally having to travel into hollowed out trees and huge fallen hollowed out logs to progress, in addition to the occasional abandoned treehouse, inside any of which it's hard to see. Perhaps these sections could include torches the player can light somehow, or something more magical to light the way. Both acts could borrow from the old Emerald Stage's gimmick in that progression isn't always entirely Euclidean and keeping an eye on your surroundings is important to progress. The spirits that live in this forest aren't dangerous, but are notorious tricksters. The badniks Eggman has placed within the forest however are much less friendly.
MFZ: Sonic and the others emerge from the forest only to find themselves mysteriously at the top of a mountain. Some sort of lab can be seen further down the mountain in the distance, but to get there Sonic and friends must traverse through the snowy, treacherous terrain they find themselves in presently. Act 1 taking place higher up on the mountain could have lots of winds blowing that threaten to push the player into the dangerous ice water. It's smart to stay on the snow and stay away from the ice while outside, but you can take shelter in the icy caves to get away from the winds, though these pathways might not be as fast a way down the mountain as taking a more direct route outside.
In Act 2, the winds let up quite a bit, not pushing the player as strongly. However, Eggman has become aware of exactly where Sonic and the others there, and has ordered his badniks to deal with them. The player must be more careful of badniks hiding in the snow or taking advantage of the slippery ice. Towards the end of the level, it becomes twilight, and then sunrise.
SPZ: Sonic and the others arrive at the Sunken Plant. It appears to have been a water treatment facility and a lab Eggman was using to produce his badnik army, and is the source of the waste he was dumping in TVZ. However, the plant has since been abandoned due to some accident that took place long ago, flooding the place with water. Many of Eggman's more water themed badniks are still here, and are still programmed to capture Sonic and the others. Most of the water sections can be avoided through careful and sometimes clever platforming, though sometimes going through the water is necessary for progression. Perhaps in some rooms, there could be a way of draining the water to make things easier, though that might cause some of the other badniks to activate...
AGZ: After defeating Eggman in SPZ, Sonic and the others follow him through a teleportation device that leads them into this heavenly place in the clouds. Eggman and his badniks are intruding on this sacred place, and must be stopped. Clouds can be bounced on Sky Sanctuary style if the player wants to take faster, more direct routes through the level, though this can be very risky as doing so is done over bottomless pits. Solid ground is still plentiful however, and is easily accessed as the slower way through the zone. At the end of Act 1, Sonic and the others find themselves entering a huge palace. Act 2 takes place inside the AGZ palace, where there are no more bottomless pits. However, the mazelike structure of the palace can be confusing. Inside the palace sometimes rooms flip the gravity upside down or shrink the player or a number of other things as a result of the mystical power within these walls. Progressing quickly is no longer an easy option, as Sonic and the others now need to work their way up the palace on their journey to the roof, where Eggman is waiting for them in his most dangerous creation yet: Brak Eggman. For this fight, Brak Eggman is vulnerable constantly, but the risk of getting forced off the edge to an instant death is ever present.
Prismatic Angel (All 7 emeralds required to enter): After defeating Eggman on the roof of the palace, Sonic and the others have successfully defended the Master Emerald. However, the seven Chaos Emeralds in Sonic's possession resonate with the Master Emerald, and a portal is opened up into another dimension, which Eggman immediately flees into. Sonic and friends leap in after to stop him, and arrive in Prismatic Angel. The first big change I would make to this level is to do away with the bottomless pits. Instead, this level is inspired somewhat by the final boss dimension in Generations, in which much of the level takes place within the alternate dimension, but sections of earlier levels appear. Sometimes, these are even mixed together in ways that are unnatural and feel very forced. Many of the level hazards and badniks encountered along your journey so far return, though in combinations that sometimes are new. Sonic and the others need to be on their A Game if they want to survive this.
Mystic Realm: Serves as the boss for Prismatic Angel. Brak Eggman returns, but this time it's been souped up. In it's new invincible state, Sonic and the others have no hope of damaging it... Or do they? Occasionally, Brak Eggman will attack, and this is an opportunity to get him to destroy some boxes containing monitors. Break an invincibility monitor, and find yourself on even territory with his power for the duration, allowing you to do damage. But be warned: He can still knock you off the edge.
Dimension Warp: Sonic exclusive fight. With Brak Eggman destroyed for good, Eggman has made a last ditch effort to beeline for the portal into this alternate dimension and lock Sonic and the others inside of it, trapping them forever. To stop him, Sonic transforms into Super Sonic. Eggman is racing Super Sonic to the end of the level, but also attacks him along the way to slow him down, which must be dodged. Super Sonic can attack back to slow Eggman down if the attack lands on him. If Super Sonic runs out of rings or fails to make it to the end of the level before Eggman, the player loses a life. Rings can be picked up along the course of the level, but are not plentiful.