I do have a bunch of ideas that could possibly expand and make this Mod more refreshing than the original:
Levels
Stage 3
There is only one thing I'd suggest to change to keep up the pace of the zone and that would be how you earn the Yellow Emerald as that Bonus Stage drags on for far too long imo. Perhaps a secret area could be worked into it, similar to the other zones? Maybe an underwater cave or a sunken ship.
Minigames
I like the idea of how they are set out but instead of it unlocking automatically after a level and paying, each Zone should contain a hidden collectable item (Red Ring perhaps?) that unlocks its corresponding Minigame permanently on the World Map, without the need to pay each time you enter.
Mission 1
Instead of having the sperm of random enemies we already have seen, perhaps have them be that of main cast males from the Sonic series, each wave being different after defeating the cock, such as:
Sonic for Wave 1, Tails for Wave 2, Shadow for Wave 3, etc.
Mission 2
As a similar idea as to what was mentioned in Mission 1, each Rock, Paper, Scissor challenge that you beat could increase in difficulty with each successful win, altering between the main cast males of the Sonic series as you progress. Obviously a defeat will still end as normal however.
Enemies
Stage 4 had a good variety, due to the fact it had Mobians. Seemed to be more fitting for this game. These types could be consistent across the game, not totally replacing all enemies we have already of course, fitting a theme for each level, for example:
Stage 1, a Babylonian Mobian, due to the level taking part in the sky.
Stage 2, an Echidna Mobian, similar to Knuckles' tribe, due to it being a dense forest.
Stage 3, an Aquatic Mobian, due to being underwater.
Stage 6, Civilian Mobians, due to taking part in the City/Casino.
** Will Expand On Ideas I Have Here Tomorrow**