I'm not calling you stupid or anything, but I didn't have any trouble understanding MGS2. You didn't really get into specifics so if there's something that was particularly confusing then I can try to make the connections for you, but it sounds like you just weren't that invested into it.
I'm assuming that you didn't play the first MGS since you were reading it's synopsis? That might be half the problem right there; this is one series that really requires you to play them in order. Each entry requires the previous one as a foundation. It limits accessibility for new players but it's also one of the things I like about the series; each entry is like one chapter in one huge game. They're much better when viewed as a whole. And as crazy and ridiculous as the story is, it's done really well.