Hello, 

I am working on a system to save the progress of the player within a level. Maybe you can take a look at my game and then on my ideas and give me some feedback. I have three possibilities in mind:

1. Checkpoints like the flag in Super Mario games
   This is the idea I find most unattractive and I see problems like: A enemy is chasing the player and the player run into a checkpoint. Then the player loads and is still chasing by the enemy.
2. Quicksave like in Shadow Tactics
   This is the easiest way for the player I think. The player has full control of it but he has the possibility to save before every challenge. I am afraid of lose the difficult.
3. Persistence of certain level elements
   When the player failed, he will restart the level but for example, opened doors and solved puzzles stay opened/solved. This is my favorite because the player cannot spam the save button.

But I thought I ask you. What do you think is the best method that makes most fun for the player? Do you have other ideas?

You could implement the checkpoints, but just saving persistent objects and the player position upon reaching one. That way enemies get reset on checkpoint reload, but doors remain open.

Another way to tackle this could be to split up your levels into their individual challenges, and just restart the scene. Right now I don't see any specific reason why the rooms would absolutely need to be connected. :)

3 is great (and is also used by “Skeleton War” here on Itch.io) but I’d only really appreciate it if there was an in-universe explanation as to why that is.