Hmmm, I think a lot of people don't get this to be honest. Bear with me.
I think to really understand what is going on with Metal Gear, you have to look at Kojima and what was happening outside of the games themselves. As ENN did a skit on, Kojima planned to walk away from the series a large number of times, but was always being forced back by the fans and demand. Metal Gear's plot is not a mess because it's deep, it's a mess because it's absolute junk that was being winged together a bit at a time as he reluctantly re-entered the arena for another piece. He used a sort of wild "conspiricy theory" type set up to deal with the problems of continueing a narrative that was never intended to go on this long and was being expanded on the fly. This created the illusion of this long, drawn out plot that had been intended from the beginning, but really if you look at what was going on with the creator this does not seem to be the case.
Another point to consider is the whole racist, xenophobia angle to the entire thing. To begin with waaay back on the NES the first "Metal Gear" was designed as a giant joke. Read the back story in the instruction booklet that comes with it, it's making fun of the politics of the time, and the entire thing is pretty much set up as a sort of mockery of the US action hero, and US exceptionalism. That said it was popular in a serious fashion for some people, who just never seemed to pay attention to the fact that the whole thing was intended to be bloody absurd as part of the joke.
Due to the popularity of the game however it spawned a sequel, "Snake's Revenge" and then later appeared as "Metal Gear Solid" about this point as the game was getting serious, a problem appeared in of the fact that the hero was a white american soldier. Something which according to some ancient periodicals was seriously annoying a lot of people in Japan who wanted to like the games, but needed a more ethnically appropriate protaganist. Enter the veiled "Switch" to the Japanese hero Raiden, who of course became very popular in Japan while the US audience wanted the original hero back. Raiden seemed to be created with the idea in mind that US audiences could accept Japanese heroes in games, but missed the point that doing a sudden switch of protaganist in a series was going to irritate fans of the original character that made the series.
As the series went on, this of course wound up splitting the Eastern and Western fan bases. One side wanted more Raiden, the other side wanted more Snake. This of course caused things to get even more involuted every single time Kojima was pulled back to the franchise since he was looking at an increasingly bizzare narrative soup that had no idea if it wanted to be serious or a satire, and real world cultural conflicts surrounding it. Debates between fans of Raiden and Snake can get pretty bloody nasty at times from what I've seen.
The bottom line is that with the final chapter, expectations had gotten so high from this mess that, there was no cohesive way of putting all of this together that would account for everything so the best solution basically seemed to be "well, it's all a lie, and anyone who could have sorted any of the details that remain up in the air is dead". This also allowed Kojima to retire Snake, but keep the franchise alive in a new form where Raiden can be focused on which will make the Japanese fans consideraly happier, and hopefully with a new storyline will cause him to be more widely accepted with the US/overseas audience.
I've played Metal Gear a bit, though I'm not a huge fan, and on a couple of points I was interested enough to read up on it elsewhere. The bottom line is that the more you know about this storyline, the less sense it makes, since key elements taken as canon can be contridicted by events elsewhere. One of the reasons why the famous hour long wrap up someone mentioned was nessicary, the only way to resolve the conflicts was to make arguements based on perspective, missing perspectives, and the hopes that nobody will notice stuff that happened elsewhere. The reason why nobody can truthfully claim to fully understand the Metal Gear storyline is because two people who "fully understand it" can argue for hours without any resolution with both being able to support contridictory opinions with elements from the game. Not even Kojima can truely answer questions about it, with authority, because it was never a cohesive work to begin with. Seriously, read the back story for the very first "Metal Gear" game, and then try and reconcile that style with any pretensions of seriousness you see later.
Ah well, enough rambling, and my apologies to whom this may offend. I do realize my comments on "Raiden" and the reasons for his creation are fairly contreversial, but that is the impression I get from some stuff I read back in the day when I was enough of a nerd to be interested in "fansubbed" (ie translated) video game and anime magazines, which incidently did a lot to change the perspective I had on Japan signifigantly.
