After talking to duckroll a bunch about the story I think I should rephrase that.
The story is ok by videogame standards. Save one thing that I have a HUGE issue with, it's a decent Splinter Cell/Uncharted/Generic Action Thriller plot that is entertaining to watch and provides a backdrop for the excellent gameplay. The comic cutscenes are fantastic and I have no problems with them.
As an MGS story though...myself being a huge MGS fan like cvxfreak is a huge RE fan...I can't help but be incredibly disappointed.
Here is the thing. Kojima is trolling the fanbase. When Portable Ops came out people were like OMG OMG OMG it's gonna be the story of how Big Boss goes from the end of MGS3 to being SEAN CONNERY in MG1. It's gonna epic and amazing story of how one man changed over the years and built Outer Heaven and METAL GEAR and how it all culminated in Solid Snake's mission in MG1.
...and then it was a little short story that was fine but took place over like a week and had almost no relevance to the main MGS timeline besides "hey, snake gets the idea to build a soldier's paradise and people start following him".
Then the trailers and info about Peace Walker came out. This time around it was originally called MGS
5. It was a real Kojima written/directed title. The trailer has Miller and Big Boss talking about acquiring a nuke and becoming an independent nation that the world is going to come after. Kojima was teasing that unlike Portable Ops that THIS TIME it'd be that awesome major MGS storyline of how Big Boss came to be sean connery and what drove him to be the boss that solid snake fights in MG1.
...and then this time again it's a little short story that is fine but has little relevance to the main MGS timeline.
While that is a bit spoilerish. I think that will help everyone who hasn't played the game enjoy Peace Walker more because it should bring down the expectations for all the MGS fans who were hoping this time was the real story deal that Portable Ops wasn't. If you don't have those expectations and you are ok with a straightforward simple action tale then it'll be fine and the presentation of it is great.
Also my biggest issue with the plot itself is that it refers back to MGS3 non-stop. IMO MGS3's plot is perfect and should be left alone. All post-mgs3 game plotlines should simply be standalone tales about big boss. They shouldn't keep flashing back to MGS3 and basing their plot around events that happened in MGS3. I find the constant need to fall back on MGS3's plot to be extremely lazy and lame. So the heavy amount of MGS3 connections in Peace Walker bothered me a lot and that combined with very little major timeline movement and a dull support cast made it the weakest kojima-written game I've played and a total disappointment from a plot perspective.
As much as MGS4's plot sucks because of it's length of cutscenes, godawful retconning/explanations, and weak ending I think I still prefer it because at least it had a handful of really awesome events, when taken separately from the main plotline. The Rex vs. Ray was badass, most of the Raiden stuff was quite cool. There's some nice stuff in MGS4 despite it's overall shitting on the MGS fans. Plus Drebin/Otocon/Meryl/Raiden were much better codec support characters than anyone in Peace Walker.
But overall I think outside of MGS3/MGS1, the MGS stories have been generally disappointing tales. MGS2/MGS4 have some neat stuff held down by a lot of superflous crap. Portable Ops is actually a nice little story but it's super short. And Peace Walker to me is just kind of forgettable generic summer action movie. It's everything you expect out of an MGS story, but nothing more and a whole lot less.
Yet it's still one of my favorite games this year because I like everything else in it