obviously nothing will really ever beat the sheer shock & amazement at how you beat psycho mantis in MGS1 or the scene after the sniper wolf battle but this is definetely the best final boss battle in MGS hands down, but there are people who thought MGS3's final battle was better. 

i perfer this over Boss vs Naked snake

I have to agree, that was an epic opening.

In terms of story: MGS1 > MGS3 > MGS2 > MGS4.

In terms of presentation: MGS4 > MGS3 > MGS2 > MGS1.

In terms of gameplay: MGS1 = MGS2 > MGS4 > MGS3.

The best final battle is obviousely 4's, it brings back so many memories.

i feel thats why kojima wanted to end it with a bang

Fixed for how I would place them.

For story, there is simply no arguing against MGS1 aside from the ridiculous retcons it introduced, but every game introduced a slew of retcons so it's hard to count that against any of them. I'd put MGS3 last for the simple reason that it's story was extremely thin. There weren't layers upon layers of thought that was put into it like the other games. The bosses in the game remain the most unidentifiable in the series because the bosses for the most part had no story to them.

For presentation, all the games are excellent. It's hard to choose any of them over the others. MGS2 is quite clearly the greatest though. The Tanker chapter was simply masterful and the Plant chapter quite literally and intentionally played with the player's mind in every single room. It's only after you understand how much thought was put into every little detail from the boss fight against Fatman which was the complete opposite of the fight against Vulcan Raven to the moral question of whether or not to kill your enemies. After MGS2 is MGS1 which probably succeeded in creating the most immersive setting due to the fact that you weren't being pulled in and out of the game like in MGS2 because the game kept playing with your mind. Next is MGS3 which is almost equal to MGS1 but is brought down by the silly unrealistic enemies. Don't get me wrong, all the MGS games have unrealistic enemies, but MGS3 doesn't even try to explain why its bosses are so bizzare. Last is MGS4 due to the lack of overall consistency due largely to its multiple chapters/settings.

As far as gameplay is concerned it's really a no-brainer. MGS1 is obviously dead last unless you're wearing huge nostalgia goggles. MGS4 is also clearly first unless you dislike diverse and intuitive gameplay as well as replay value. The only real placement I should have to explain is putting MGS2 over MGS3. To explain that I should only have to point to Snake Eater's attrocious camera that was not designed to be used well in the game's environments whatsoever. But what's that you say? Subsistence's camera voids this? Well that's not all that puts MGS2 above MGS3. MGS3's menu system was a chore. Everytime you had to change camo. Everytime you had to remove bullets and heal injuries. Pretty much everytime you entered into a new environment, you'd have to press start, wait two seconds for the screen to load, and navigate through a series of clunky menus, and wait two seconds after you finish for the game to load. This woudn't have been such a big deal if not for the fact that you had to do it so very often. The clunky CQC controls were also a detraction. All these problems were solved in MGS4 further adding that it has the best gameplay in the series.

To be honest, MGS 3 and 4 are EQUALLY the Best Intros. Both are just so amazing really.

And at the same time, Boss vs Naked Snake and Solid Snake vs Liquid are EQUALLY the best Boss fights in MGS series.

MGS3 main theme is still the best in the series. And that says a lot.

In MGS4, when I saw Raiden in the Ninja suit, I went like "Come on! Why can't I be him now?!"

?????????????????????????????????????????

You must be kidding?

Story: MGS2 > MGS1 > MGS4 > MGS3

Presentation MGS1 > MGS3 > MGS2 >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> MGS4 (i almost fell asleep between act 3 and 4 no kidding)

gameplay MGS 3 (still best today) > MGS1 > MGS2 > MGS4