The thing about Metal Gear is that Kojima was basically making a movie narrative out of them and there was a lot of political references. A shadow organization that controls everything, proxy wars and private armies working on contracts, biological weapons that can target specific genes in people, using brainwashing on kids and advanced medical testing to create super soldiers(basically trying to make another Big Boss), behind it all was a group called the Patriots who's goal was to keep America on top but nobody knew that the Patriots was actually just an AI program now that learned how to make the most profits...the war economy. Constant war made the most money and the cycle never ended. The goal of Solid Snake was to break this apart so people could just be left alone. No intervention from a shadow government disrupting people's lives. Before that, Big Boss wanted to create an army outside the boundaries of any Nation. He was tired of soldiers doing the dirty work of politicians and not asked for their opinion. Ultimately he was wrong, doing that only made him and his men a bigger target from all sides.
There's some smaller stories about individual characters weaved into it(Big Boss, The Les Enfants Terrible project, Dr. Emmerich, Raiden) but my guess is that Kojima felt the best way to explain the greater narrative was with cut scenes.
With MGS4 the whole series was wrapped up in the ending. With MGS5 they went back to explain what happened before Metal Gear 1 on the NES. It's actually quite interesting if you have followed the story along all this time how it went down. Things you thought you knew turned out to be false. You could write an entire book or series with the amount of info and characters in these games. I think that's the problem for many people, there is just too much to keep up with and it gets lost.