I think MGS4 had legitimate, mechanical problems with regards to gameplay & story handling; specifically the Boss fights & their backstory. In previous MGS games, a flashback or monologue by the boss was enough to hint at a depth of character; in MGS4, for whatever reason, they abandon this approach, and make Drebin tell you a trite ghost story about each of them. Yes, you can reason that for some reason, each of the Beast's were too "traumatized" to make a monolouge, or whatever, so why not use the "press x for flashback" to show a series of scenes that show a child going through tough & screwed up times that also led to a scene of each of these Beast's putting on their suits ? I still think that would've been fa more efficient than hearing Drebin talk about them.
Drebin's importance is also erratic; it takes 5 mins for him to introduce himself as a gun launderer? From a directing point of view, this is a failure, because he does not become *that* important later on; yes, his role is obviously not what it seems from the second you see him, and they explain this in the ending (during the wedding, the scene with otacon), but still, it should've taken a minute to get that point across.
Otacon was also written sloppily, and similar to the almost "drama for the sake of it" step-mom admission in MGS2, Kojima for some reason decided to take a logical & funny sexual fling with Naomi (come on, amid all the story, it's obvious sex for pleasure wouldn't really factor in, especially with scientists), and make it into this bloated emotional affair. Yes Naomi has backstory from MGS1, but she & otacon never worked on the same team back then, nor since. Kojima also seems to get confused with whether Otacon & snake should feel betrayed by Naomi, although with Snake it's more obvious he's next to indifference (possibly because Naomi's backstory has little importance with him trying to kill Liquid Ocelot) as she explained herself to him in the previous MGS1, and Snake even understands her reasoning and more or less can't blame her (that's what I remember from MGS1, anyway).
Back to Big Boss however, yes it can be viewed as fanservice, and too sudden (even for Kojima) of a plot-twist that some will just go "No, thanks" and ignore it. However, you have to remember Kojima wrote himself into a hole with MGS2 (despite how great many may think it is), especially with the Liquid arm thing. Would you want MGS5 & MGS6 beating a dead horse by keeping Snake alive to explain everything that happened in the de-briefing of MGS4 over the next decade? Really? Because it seems as much as some will rant about MGS4 sucking, just as many will say "if snake is alive in MGS5, that's it, I'm not bothering anymore." Kojima's choices about MGS2's story obviously had an impact on the rest of the game's in the series, and he made a judgement call to explain / begin certain things (MGS3) & explain / end almost the entire thing (MGS4).
I may be one of the few that thinks this, but, I was relieved the de-briefing occurred & explained the rest; I was further relieved that BB finally did die, in a legit fashion due to FoxDie. I say legit since Kojima obviously felt Liquid being somehow alive despite dying from foxdie was ridiculous to do (thankfully this was explained as well, but further reinforced by the Database too), and it's logical to conclude if anyone else died from FoxDie, it's safe to say that they are dead period. I also thought that Ocelot carrying on the personality of Liquid fully reinforced some central concepts with memetics & the meme, and would've been a lot more appropriate than Ocelot having mystical powers, and yet, never used such abilities in previous outings in the MGS saga (despite his father being The Sorrow & supposedly having those abilities; I say supposedly because the backstory of MGS3 hasn't been entirely explored just yet.)
Regarding how snake getting a cure would've been less absurd than FoxDie competing with FoxDie, it depends on how you look at it: if there was a foxdie vaccination, why didn't Big Boss use it? Or anyone else for that matter? The FoxDie vs. FoxDie concept, while can viewed as an "easy" fix, does fit with MGS1's theme of gene's competing with one another to be expressed, as well as natural selection. It also reinforced Drebin's ulterior motives (and prevented a stupid scene of Drebin injecting Snake with whatever, who somehow let's him do this) for the <B>Patriots</B>.
This also reinforced the fact that despite being used in MGS1 (inital vector for FoxDie) and in MGS2 (Tanker incident blamed on him, Solidus taking his name for the Bigshell Hijack, Raiden using his name as a code-name), Snake is still a soldier who is still being used, and at the end does he finally escape all of it with the closing of the story, the end of the <B>Patriots</B>, and the inevitability that he will die, and that he should try & make the best of it since he no longer needs to fight & be a soldier anymore.
Solid Snake getting cured & being young again, hm... I'm sure if that happened, he would've totally retired, not return for future games, upon which, no one would ever complain that Kojima should've killed him off, or made him unable to return, because the games somehow suck. Kojima obviously felt the story of Snake went on long enough, whether or not he should've been killed is irrelevant since he's 'alive, but going to die" in the series, and it just gets to people that it's completely out of their hands because it didn't follow their idealistic expectations.
The idea that MGS3 was created as fanservice (which was hinted at with the idea of playing as Big Boss as unnecessary) seems a bit flimsy to me, as MGS3 focused on a more suitably simplified story since it was obviously made for the intention of showing how everything in the MGS storyline began. MGS3 was almost required in order to help make sense with some of MGS' backstory, which still had plenty of holes & questionable things to it, where some make it seem as if MGS4 is the only game that has this while they feign outrage & lolz.
At this point though, I still stand by that editing could've improved the story in MGS4. Hell, I was rather surprised they didn't take the route of releasing the game in 2 different parts, sort of like a double album, but that's assuming that an MGS4 substance won't come out and offer more gameplay and/or story. Until then though, there always a possibility for a fan-edit of MGS4's CG
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If Big Boss handn't showed up, confirming the questionable nature of his remains that shadowed MGS1 & MGS2, and also explains why his remains couldn't just be "handed over" (a fairly big annoyance with MGS1 to this day, for me), and then they used some other character, you would hear countless bitching about "What? Otacon/Drebin/Naomi's Video/Liquid/ explains everything? Whtf, this doesn't fit into my previous assumptions, this sucks!".
Taking the point of Big Boss showing up and countering what Naomi said was true, I disagree somewhat, as Naomi (as far as I can remember, I've skipped the cutscenes on the subsequent playthroughs of MGS4) did not explicitly say that FoxDie would counter FoxDie, and that Snake didn't need to kill himself, etc. She gave him a timeline of up until when shit would go down and Snake might become a weapon, but then again, it can be argued that the whole thing regarding FoxDie mutating like that can be absurd too. It can be further argued that Naomi largley did not need as many scenes as she did, too (the whole Naomi & Vamp thing, while Vamp being there at all and doing nothing more than henchman stuff, after developing him in MGS2, was silly).
If you're gonna call certain things MGS4 absurd, I see no reason why not to possibly consider anything else absurd too, like Sunny coming along & supposedly being important, yet, kind of like Naomi, her scenes ultimately felt underwhelming, and Sunny's "importance" wasn't as important as previously suspected (I know I wasn't the only one confused with the behind the scenes hinting that Sunny was very important to the story, yet when they compare that to MGS4's actual story, it isn't quite clear). Rosemary returning with her pointless codec convos about Psyche were also absurd, especially since Codec wasn't used nearly as much, and all the excess Otacon-guiding you had to hear when knowing full well where to go & what to do that wasn't in the codec (and therefore wasn't optional to skip listening to), was also absurd & stupid.
The arguments over where the MGS series should've done this or that are moot, imo, as none of us are in a position to go back and change things, nor retcon them, unless someone high up at Kojima Productions is happening to read of this (highly doubtful). That also being said, it would silly to use elitism to shut off other's ideas & opinions as somehow "wrong" to the series, when the best any fan of the series can do is analyze, argue, & gripe about what actually ended up being in the games.