Your modification proposals are really well thought-out and detailed, fantastic job! I'm really looking forward to playing your finished product.
The best advice that I can give you in terms of level design would be to make sure that each level has some sort of unique identifier. New types of challenges, enemies, obstacles, or powerups can massively help with this. Putting some time into playtesting and differentiating your levels (to figure out, from a player's perspective, how the level plays) can also give you some direction in how to design things.