Ok. I have only played MGS3 and MGS4, so I don't get the whole thing (I kinda wiki'd the rest), but I will say that I never really bothered to get it. Also, I think some of the things in the series were just bad story telling.
Yep, you heard me. No, do not start crying, I am stating my opinion and bashing and whining will not cause me to change or open my eyes.
You are probably not the only one, just one of the few. I played 3 and 4 and never skipped a scene. And I will say this: screw the storytelling and design of this series!
The first two missions in MGS4 were awesome. Large areas with lots of bad guys, hi-tech gadgets, and it challenged me to think about stealth. However, by the third level, half of it was a rail shooter. The level in the snow base was only interesting when you fought Vamp, and the carrier mission, while climactic, was no good to me. And turning the game into a fight scene at the end without any controls? WTF!?!
Anyway, what I disliked was the ending. Don't get me wrong, I love twist endings in movies. In fact, I love the Saw movies for the twist at the end. And yes, MGS3 and 4 do pretty much the same thing. But there is a difference.
In Saw, the directors got the twists right (except six, I still don't get that one). To me, it did the twists right because of camera positioning. Ever seen Saw 3, maybe Saw 2? Well, I loved the little flashback scenes. But I love how all they did was show you things you had already seen, and then panned the camera a few meters to the side, or let the shot linger a moment longer so you saw some important plot device that was hidden just off camera earlier. Oh, and if a good guy is found out to be actually bad, they didn't make him sympathetic in the first place. You were horrified because other characters you knew were now in danger.
When you boil it down, the twists were good because the audience could relate to it. If you sat through the movie, the twist made sense because it showed you what you had already seen, and then changed the angle to put it in new light. Good characters being bad? It was ok because we had already seen what they could do and had not started to cheer them on just yet. And if we did, there was always someone else for our sympathies to side with.
*SPOILER WARNING*
MGS pisses me off because at the end, it has someone tell you everything you knew originally was wrong. I was pissed! I felt like I was a puppet! The whole time I was doing this, I had come to believe in my mission, hate the bad guys, love the good guys, I had no problem kicking Liquid Ocelot's ass. The day was saved, I was satisfied, and I could move on with my life. Sure, a good guy may have died. Maybe my character was emotionally hurt, but it was still good at that point.
I don't want some character to then turn to me at the very end and say that I had just killed my foster mother not because she was evil, but because it was a PR stunt. I don't want to know that I was set up not to kill a man because he was evil, but because I was gaining someone else entry to the hi-tech doohickey.
In Saw, you never felt like a puppet. Information was witheld to keep you guessing, but you could still see hints throughout the movie. In MGS, there is nothing. No hints, just witheld information. Everything you believed was a lie and I hated the game for that.
Oh, and I feel like being rude, so I'll say this. The final cutscene in MGS4 is an old man blatantly telling you all this for an HOUR. And he is supposed to be dying. It is the only instense in my life where I wanted a character to die so he would shut up.
So, no, you are not the only one who gets the story. It's just that some people were upset.