I think that you're headed in the right direction with your modifications, I do have some questions
- How are you planning on making your levels unique? 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.
- When you reskin your enemies and players, and add new animations, will the sprites be custom-made? I'd highly recommend this, as it'd make the change much more significant.