Okay, as much as I love this game, the story, the addictive pokemon-like nature of kidnapping troops... I now have a few story related problems. This game's plot simply breaks the MGS story, and punctures holes in the plot the size of my fist. I'm not really angry about it, but it's bothered me because of how well connected the story of all the other games seemed at that point. Especially if your point of reference is that official MGS database they have on the PS3. 
 
And, really... all of it could have been avoided if snake didn't call his base Outer Heaven. But he did. According to the database, it was founded in the 90s (instead of the 70s, here) by Big Boss, and in South Africa, not the caribbean sea. Kinda wierd, but I could roll with it. Yet another problem though is when the Database mentions he formed FOXHOUND with the CIA, and had been leading it in some form or another till the 90s. I thought this whole game was about how he's turned his back on the government for making him do what he did, and whatnot. Just a lot of things like that, that don't really add up at all. 
 
Whatever, it's not a big deal, it's just that MGS 4 wrapped everything up so tightly, that inevitably any sequel would have messed a lot of things up. Oh well. Maybe it's better that MGS continually confuses everybody, and remains a mystery. More fun that way hahah.

It's Kojima, he can retcon the entire series and no one would care.  Just let it go, and take in the new retcon.  >.>

You're asking too many questions. After Ocelot's mind was taken over by Liquid (and then it turned out it wasn't), I just stopped trying to make sense of it.  
  
However, I too was a little miffed at Outer Heaven being a sea base, because in the original game Outer Heaven is clearly on land. However, it's possible that in the 20-ish years between Peace Walker and Metal Gear they moved.  
 
And just wait until Rising comes out. I'm sure that will find tons of new ways to mess up the continuity. 

ahahahahahaha MGS story making sense... omfg hahahaha.... hahahaha ohhh boy.... hahahahaha 
 
Ah, thank you for this.

I have to disagree on this one.  
 
It could very well be another Outer Heaven that was made in Zanzibar Land.   
And all the Metal Gear's had other names attached : Rex, Ray, Arsenal Gear, Metal Gear D, etc.  
The important thing to remember is that Peace Walker is the turning point for Big Boss, so there is still story left to tell.  
Plus ******SPOILER ALERT!!!******  At the end of PW, he does save the U.S. from starting a Nuclear War, making friends with the brass again. Who's to say he won't use that in the future to help out his own agenda. He took the word of the KGB for crying out loud! 

" I have to disagree on this one.    It could very well be another Outer Heaven that was made in Zanzibar Land.   And all the Metal Gear's had other names attached : Rex, Ray, Arsenal Gear, Metal Gear D, etc.  The important thing to remember is that Peace Walker is the turning point for Big Boss, so there is still story left to tell.  Plus ******SPOILER ALERT!!!******  At the end of PW, he does save the U.S. from starting a Nuclear War, making friends with the brass again. Who's to say he won't use that in the future to help out his own agenda. He took the word of the KGB for crying out loud!  "

Didn't think it was possible to break the story. Really, something happened to throw off the gay immortal vampire/ mind controlling arm/ ninja cyborg/ Im dead Im alive Im dead timeline?

Well it's been proven that only Leigh understands Kojima. Maybe you should ask her to clear things up for you.

" Okay, as much as I love this game, the story, the addictive pokemon-like nature of kidnapping troops... I now have a few story related problems. This game's plot simply breaks the MGS story, and punctures holes in the plot the size of my fist. I'm not really angry about it, but it's bothered me because of how well connected the story of all the other games seemed at that point. Especially if your point of reference is that official MGS database they have on the PS3.  And, really... all of it could have been avoided if snake didn't call his base Outer Heaven. But he did. According to the database, it was founded in the 90s (instead of the 70s, here) by Big Boss, and in South Africa, not the caribbean sea. Kinda wierd, but I could roll with it. Yet another problem though is when the Database mentions he formed FOXHOUND with the CIA, and had been leading it in some form or another till the 90s. I thought this whole game was about how he's turned his back on the government for making him do what he did, and whatnot. Just a lot of things like that, that don't really add up at all.  Whatever, it's not a big deal, it's just that MGS 4 wrapped everything up so tightly, that inevitably any sequel would have messed a lot of things up. Oh well. Maybe it's better that MGS continually confuses everybody, and remains a mystery. More fun that way hahah. "

I think Kojima's probably going to remake MG sometime later
all things introduced in peace walker makes sense in terms of the MGS timeline
but it's still hard to see how BigBoss in PW transit into the BigBoss in MG