You might be on the right track with just removing the scene types. Since there is a mechanical reason to keep the scenes themselves. Maybe instead of combat or social scenes, you could have high energy or low energy scenes. The more energy in a scene the more stamina points the players have. This would make some sense seeing how people feel social pressure to act in a specific way in specific settings. It makes even more sense if the purpose of the game is to simulate book or film of cyberpunk settings.
In that context, the scenes could be very useful. The high or low energy scenes could be optional also. If the GM doesn't want to deal with it, just leave Stamina as is.
Extra stamina could also be used to reward the players for working with the GM's story. Not explicitly, just that a GM prepared scene may have some extra to up the energy. If the players define a scene, they don't get any extra.
You don't have to do it that way, that's just a way of making the scenes variable and functional.