THIS!!! ^ ^ ^ ^
Put your UI in its own scene.
Put your player in his own scene.
Put your level content in its own scene.
Have the actual scene only be a little slim trim and sugar-free game manager stub construct that loads all the other scenes additively.
Additive scene loading is one possible solution:
https://discussions.unity.com/t/820920/2
https://discussions.unity.com/t/820920/4
https://discussions.unity.com/t/824447/2
A multi-scene loader thingy:
My typical Scene Loader:
Other notes on additive scene loading:
https://discussions.unity.com/t/805654/2
Timing of scene loading:
https://discussions.unity.com/t/813922/2
Also, if something exists only in one scene, DO NOT MAKE A PREFAB out of it. It’s a waste of time and needlessly splits your work between two files, the prefab and the scene, leading to many possible errors and edge cases.
Two similar examples of checking if everything is ready to go: