So I had been giving updates for someone coming into this series completely blind, starting with Metal Gear on MSX and going all the way through. I was at MGS3 (specifically, right around meeting Granin), but other things came to my attention, other games came out, etc, so I put MGS on hold.
Well I went back, started it over, and ran through recently and it was the shit. Great game. I liked the new health system quite a bit, as well as the more expansive environments. Something that really impressed me were the boss fights. The End was a really fun fight, and though it was really easy in my opinion, it was a great subversion of the typical boss. The Boss herself was one that was interesting because I played it a handful of times and got my ass handed to me, thinking that the fight itself was cheap. Then I came back to it the next night, took things a little more methodically, and beat her the first try. It's like her little teachings were working. :O
The story is still fucking bonkers at this point and the anachronism is pretty hilarious especially in this one (Kojima just really had to get a RotJ speeder bike chase homage in a 60's period piece, didn't he?). It's basically endearing at this point, just take the ridiculousness for what it's worth. The core story of 3 was....eh, mainly because characters like Volgin and EVA just weren't that interesting to me, but the relationship between Snake and The Boss was well written. I didn't really post any thoughts about the story of MGS2, but the way it smashed the fourth wall to smithereens was executed pretty well. The absurdity really worked in that one's favor well.
The best part about this series to me is how each game basically excels in a different field. MGS1 might just be the best pure "game" thus far, and certainly has the best standalone story. MGS2 is a very well put together satire on video games and sequels in general. Playing MGS2 right after playing stome VR Missions because the Raiden character did the same thing. And then MGS3 finally makes the best use of the stealth abilities that Snake has, and has some interesting, if simple, messages about the soldier's role in war. If nothing else, I totally want to do a replay of these games sometime once I'm caught up, mainly because of the crazy attention to detail on things. I really have no idea what my "favorite" would be since each one is so different and enjoyable for different reasons.
Btw, The Legacy Collection has been one of the best gaming deals ever. Gad damn.