Metal Gear would absolutley destroy the foundation of war as we know it. It's, as stated, a Bipedal nuclear weapons system. This would create all kinds of issues as it would give it's controller the ability to launch a nuclear weapons attack from anywhere on the world. In addition, it's mobility completly takes the 'range of the missile' out of the equation as it could just walk within range after being dropped off where-ever it needs to be.
While nuclear subs have this ability to some extent, Metal Gear takes it beyond just a step further. Subs are much easier to find. Metal Gear is, indeed, covert, as it is so small, in addition to it's other attributes, that it could be easily hidden from enemy detection until needed. IE: in an underground bunker. Most detection methods are designed to find an object that is either much larger, or (speculation here) designed to give off a much stronger heat signature.
The "connect infantry with artillery, making it invulnerable to firepower shortages and terrain" part of your question I daresay is the easiest to answer. It's a mechanized battlesuit my man. The very DEFINITION of next-gen warefare. Militaries all over the world (in real life) have been trying to create this very thing, or something similar to it at least, for years. Do you have any idea how much ammo weighs? Or how much more that weight feels like after youve patrolled on foot for twenty clicks? Or how much for that matter your ARMOR's weight feels like and is? (anti ballistic vests and such)? -- And terrain is a JOKE. It dictates everything about everything we do as soldiers. We are not hindered so much by our equipment, physical fitness is the counter to that, or by our enemy, superior tactics and know-how counter that, but terrain is un-conquerable. It either allows or denies a mission with absolute authority. Climb a few clicks up a mountain because it's in your way and then tell me different. Metal Gear (or just about any mechanized battlesuit for that matter) COMPLETLY eliminates any kind of hindrance from everything I just covered here. Sure its ammo is feasibly exhaustible, but when you have a hard time carrying 60-80 extra pounds of rounds, having SEVERAL TONS OF IT at your disposale changes the game in a whole new way.
Afterthought: I have since learned that my idea of how subs work was sadly mistaken, but the basic premise of my answer remains sound. I'm going to leave the answer as is.
Many of the older games in the Metal Gear series were released before the modern trend of pre-order bonuses and collector's editions and such. All of the following games
- Metal Gear
- Metal Gear 2: Solid Snake
- Snake's Revenge
- Metal Gear Solid
- Metal Gear Solid: Integral
- Metal Gear: Ghost Babel
- Metal Gear Solid 2: Sons of Liberty
- Metal Gear Solid 2: Substance
- Metal Gear Solid: The Twin Snakes
had no pre-order or collector's edition content of any notable form, in any version or format they were released in (that I'm aware of or have been able to track down).
Metal Gear Solid 3: Snake Eater was the first game to have such content. The original Japanese release (which shipped after the North American release) allowed you to download a unique camo skin, and there was a limited-edition package for sale in Japan that included some physical extras. Pre-ordering in Japan got you a disc with some extra camo skins on it as well, in addition to access, via cell phone, to a site offering downloads of images, music, and more camo skins. The European release of the game included some extra gameplay modes (a boss rush mode, cutscene replay mode, the "Snake vs. Monkey" mini-games, and some facepaint camo).
The majority -- or possibly all -- of these camo skins and features were made available in the Metal Gear Solid 3: Subsistence re-release. Subsistence includes the first major piece of content you won't be able to access any longer: it shipped with a multiplayer mode called Metal Gear Online, which was discontinued in 2006 is is now unavailable. Limited-edition copies of Subsistence were also sold with some extras, mostly videos and documentaries and the like.
Metal Gear Solid 4: Guns of the Patriots had bonus packages that mainly featured physical items, including a bundle with a special PS3 with a unique color. None of the bonus content was gameplay related, it was all stuff like documentaries, figurines, and soundtracks. Guns did, however, re-introduce a Metal Gear Online multiplayer mode, which was subsequently shut down in 2012. So you can't play that any longer.
Metal Gear Solid V: Ground Zeroes was basically a glorified demo, and as such didn't have any real bonus content associated with it. However, it itself unlocks some content in Metal Gear Solid V: The Phantom Pain via save data upload.
Metal Gear Solid V: The Phantom Pain had some cosmetic items made available to players who pre-ordered it (at least on Steam, I'm not sure about other platforms). You can upload your Ground Zeroes save data (again, at least with the Steam versions) and unlock some extra characters for use in your base operations in Phantom Pain. Presumably at some point the backend for that data exchange may go down, at which point this would stop working.
Similarly, Phantom Pain has an online mode, which launches in October. Given Konami's track record, you can expect this to eventually be shut down. Similarly MGSV's "forward operating base" game mode... which I don't know much about but sounds kind of like Clash of Clans-esque base raiding? is backed by servers on Konami's end and will eventually be sunset.
Metal Gear Acid didn't have any interesting extra content, but it's sequel, Metal Gear Acid 2, came with a physics stereoscopic lens add-on that might be difficult to obtain now, although you can probably easily find a suitable workaround.
Metal Gear Solid: Portable Ops had a pre-order package with some extra camouflage and such. The game had a peer-to-peer multiplayer mode, which still functions (as far as I am aware), although you'll need to find other players to actually play it. Metal Gear Solid: Portable Ops+ expanded the online mode but otherwise offered nothing new in the way of content you might now miss.
Metal Gear Solid: Peace Walker didn't have any bonus packages, but does have a multiplayer mode. As with Portable Ops, I believe this mode still functions, so all you'd need to experience it is friends.
Metal Gear Solid Touch is an iOS game, and as such can't have any kind of pre-order exclusive content. It was only release for select regions, though, so if you're not in those regions you cannot buy it.
Metal Gear Arcade is interesting, and not a game I'd heard of before researching this question. It was only out in Japan, so it's something you'll miss (potentially) in that sense. It was also basically an arcade version of MGS4's online mode, and consequently may not be running any longer. It appears that the game used head-tracking controls, which might have been fun.
Metal Gear Solid: Social Ops is another game that's only available on mobile platforms in Japan. It was a sort of mash-up of gameplay from other portable Metal Gear titles, and backed by servers that Konami shut down in 2013.
Finally, Metal Gear Rising: Revengeance had an assortment of physical bonus or collector's items, but nothing really gameplay affecting. There are versions of the game out there that include all of it's associated DLC.
So basically, the major content that you can expect to be missing out on by playing through the series today is either not gameplay-affecting in any major way, or was multiplayer in nature. And frankly, console online multiplayer being what it was in the age when the associated games were released... you aren't missing much.
Best Answer
Metal Gear Solid is notorious for being tricky to follow.
Probably the easiest approach is to go in order, MGS1-4. Some events in MGS1 call back to the MSX games, but MGS1 can also be read as attempting to remake those games. MGS3 is somewhat disconnected from the rest of the narrative, so it's not necessary to play it after the previous two games. Whichever way you play it, be prepared to not follow all of it - there's frequent allusions to events that you're not likely to know anything about, and this is part of the territory.
There are no plot differences lore-wise between Twin Snakes and MGS, so whichever is easier to access. The two games have a different script (Twin Snakes is a bit sillier) but Twin Snakes doesn't add in new dialogue to tie it to the later games better or anything like that.
There's also a compendium available on the PS3 that explains the lore a bit more.