Games that segregate their stories from their gameplay such that one is always interrupting the other tend to fall pretty flat with me, even if the writing and film-making are superb in isolation. You can't take a great movie, chop it up into scenes, and force the viewer to jump through mechanical hoops to get to the next scene and claim you haven't made that story dramatically worse, if not outright ruined it. Games like that would just be better off being movies or TV shows, imo. The only way they could compare favorably to great works in other media is if you completely ignore and discount the game part and how that enhances or undermines the narrative--the analytical equivalent of those youtube videos that compile the cutscenes of a game into a "movie" with most/all of the interactive bits culled out.
This is generally how I feel about stories in video games. I tend to prefer ones that don't over-rely on cut scenes. There have been video game stories I've enjoyed that are mostly cut scenes, but for the most part that enjoyment has been independent of the gameplay, like a pretty good movie or TV show stapled on top of a pretty good video game but never really interacting with it.
I felt like The Last of Us didn't need to be a video game to work. It was a typical post-apocalyptic drama put on the same disc as a typical third person action game, its set pieces not as memorable as the ones in Uncharted. Uncharted in itself is just an action adventure movie stitched between a bunch of interactive set pieces, but you have to admit those set pieces tell an exciting story on their own, like a roller coaster.
Metal Gear Solid 3 is essentially a really good seinen anime stapled on top of an entertaining radio drama stapled on top of a good stealth video game.
Yakuza's cut-scenes could be an entertaining J-Drama on their own. The game by itself, which really includes all the side stories, still however make for a unique and entertaining virtual tourism simulator filled with well-written short stories.
I'm more impressed by interesting video game stories that are actually told through the gameplay.
Soma is some really interesting subject matter that couldn't be done in anything other than a game and have the same impact. How it measures up to a movie depends on the writing I guess. The same goes for 999 and Return of the Obra Din.
If you go back to older or more traditional-style point-and-click adventure games maybe some of that stuff could stand up to most literature: The Shivah, I Have No Mouth But I Must Scream (which is based on a book), Charnel House Trilogy.
How does Half-Life 1 measure up to action movies?
RPGs, particularly big-budget 3D CRPGs, might be a bit harder to describe but I don't know: How do you think Mass Effect 1 would measure up to a show on Syfy? It has a lot of short cut scenes but they're interspersed with dialogue options that affect the plot. CRPGs that rely on cut scenes less or not at all are less ambiguous here, like Planescape Torment or Fallout New Vegas.
The Witcher 3 is a really weird one. Does it have a lot of cut scenes? Yes, but those cut scenes could probably not stand on their own narratively. Like Mass Effect, they're connected to and affected by dialogue and gameplay choices. And more importantly, the side quests in Witcher 3 feel very close to Sapkowski's original short stories that inspired the game.
