The answer to the topic question is simple, 95% of the time it's due to shitty game design.
For instance, I played Black for the first time the other day, the opening sequence took forever.
And what was this opening sequence comprised of, Final Fantasy quality CG, a long intro? Nope, it was just a (really) slow changing white text on the bottom left corner of a black screen with an obnoxious "heroic" orchestral tune in the background... Then came a shitty live action intro, which was unskippable as well, like all the other cinematics in the game, and once the oh so captivating video stopped, a load screen kicked in, just to load the menu.
As a side note, Criterion guys are geniuses when it comes to coding a renderer and toolchains, but they really could use some help on the user interface side. All the Burnout games had stupid user interfaces (especially the way the games handled game saves), Black is no exception.
To get back on topic, I'd say that some game designers take the "action movie you play" mantra way too far and way too literally. Sure that cinematics add to the whole experience, but a game designer should think, first and foremost, about the game design, not the story telling.
In other words, if a situation forces a game designer to chose between story telling or the game mechanic, the latter should always be the priority.
That said, I don't see why a good game designer can't mix the best of both worlds - by making the cinematics skippable using a two buttons combination, e.g.: start, than Y/triangle -, unless of course a technical reason makes it impossible, in which case, it still possible to tell the end user that the game is loading when he presses the start button and then let him skip the rest of the cutscene as sson as the next level/room is loaded into the RAM.
Speaking of stupid game design choices - and while I know it's OT, that's why I won't address this subect for too long - I want to say it once again, crappy implemented stealth missions do not bring any variety to your game it brings only hate to it. My hate, amongst others', I'm sure.
Stealh sections this generation, are like the racing sections in action games back in the days. With the difference that most racing parts from the games of yore didn't use to be as bad as today's stealth ones.