I'm always curious about Feature Flags - I'd love to use them.

But they only seem to work if the interface doesn't change. From the example you gave:

    function reticulateSplines(){
      if( featureIsEnabled("use-new-SR-algorithm") ){
        return enhancedSplineReticulation();
      }else{
        return oldFashionedSplineReticulation();
      }
    }

All well and good as long as the enhancedSplineReticulation returns the exact same structure that the old one did. If it doesn't, then a bunch of code that handles the new reticulated splines also needs to be behind a flag (because the structure changed). And that could mean a chunk of UI needs to be duplicated behind a flag because it changed, and so on.

How do you use feature flags when the features aren't just trivial changes to methodology, but affect multiple parts of the system?