First of all, the cut scenes are part of the appeal because the story is massive, second, you do not have to stand up when getting out of cover, that is a blatant lie, and three, you don't have an infinite supply of tranqs unless you're playing on baby mode.
Last time I checked, MGS4 was supposed to be a video game, not a collection of feature length movies. Decent story telling isn't about quantity, it's about quality. A skilled author would be able to condense their ideas into something more fitting for interactive media. HL2 (a game praised for it's storytelling) never even has a single cutscene hence retaining immersion.
As for the last 2 things you mentioned, I am not really sure what to say. Yahtzee is a mature gamer with plenty of experience so I doubt he would make a mistake about that. In regards to the difficulty, not everyone is a masochist and you shouldn't have to crank up the difficulty to have fun in the game or make the experience any more realistic.
Good job on crying about it though. Shows how much you love the game despite it's faults.\
EDIT: Looks like Yahtzee has been sucking too much richard lately.
How has he been sucking richard lately? His job is to criticize games, not to take pay outs from game developers just so he gives their latest work a high score. If anything his honesty is refreshing. Sure you might disagree, I loved Oblivion and Assassin's Creed, but he ate them alive. You learn to live with the good and the bad comments. He tells it like it is and his videos are entertaining.