I apologize for any incoherency, for I am falling asleep as I type this.
The key point of any commercial game is fun. A large part of making it fun is proper pacing. This goes for pen and paper games too, not just videogames. Imagine if you were playing DnD and suddenly the Gamemaster forced you to listen to a 10 minute monologue he gave. You'd probably think he'd gone mad. Cut scenes like this ruin the pacing because there's nothing you can do while the cut scene happens. You suddenly go from being an actor to being part of the audience.
Action games have set it up so the problem of cut scenes would be hard to remedy, because players are trained to try to kill anything that moves and are regularly punished for not doing so. So far the most used remedy seems to be to simply make vital characters immortal unless the plot demands they die. Players are rarely allowed to interact with hostiles in ways other than attacking them unless the action is handled through a break in the game where the plot takes over the character's actions. Many games also have it so nonhostiles can only be interacted with by dialogue, preventing the use of violence as a means to and end.
A good GM can react to player actions and react accordingly. Videogames attempt to form plots like movies where there are few, if any, plot changes the player can effect. You are regularly removed from a participating role when the plot demands it. You are not allowed options you would have if the game truly allowed improvisation.
Part of the reason for not allowing more options is that this discrepancy becomes more noticeable as games become more realistic. Suddenly you start to wonder why the game world doesn't allow you do do things you could conceivably do in the real world. Whether it be claiming you're pregnant in a social simulation to create drama, or to talk down or surrender to your enemies in an action game, or even to simply destroy a locked wooden door or jump a chest high fence. When the game doesn't pretend to allow options the invisible walls don't bother people as badly. They're still there, but they make sense with the game's logic. Imagine a DnD game where the GM only allows you to go to certain points in the world and chases your character back to those points with a T-Rex if you attempt to go elsewhere. You'd probably feel that you're not playing your story, you're playing his story. This is where Videogame stories are right now. You're not playing your story, you're playing Hideo Kojima's.