a lot of people seem to have this conception that linearity is strictly worse than nonlinearity (see Mark Brown's "Boss Keys" youtube series... or don't because they're pretty flawed conceptually)
linear and nonlinear progression both have their advantages and disadvantages, which I touched on in my "What's So Great About BOTW?" blog. Knowing those differences, a good dev will step in when necessary to keep momentum going and keep the player feeling like they're progressing. I think an example of this done badly is Death Stranding, where the opening gameplay is constantly interrupted by 20+ minute cutscenes. There are a few moments where zelda in particular (not just skyward sword, though people love to rag on it for no real reason) will have camera movements or the helper character point out something totally obvious, and breaking the flow of gameplay in the process. It's pretty minor though so I'm okay with it when it happens (not just in skyward sword, but twilight princess and oot as well)
Dark Souls does this really well, as the most significant moments will lead to smooth transitions between gameplay and cutscenes, and the cutscenes are always really fun to watch without getting too long, but not all bosses even have introductory cutscenes, so the flow of gameplay in dark souls games are very good