As I explained in my article The Long, Dark Path to Metal Gear Solid 4, Kojima's relationship with the Metal Gear series has become increasingly complicated ever since MGS1 raised stubborn expectations about what the series should be in the minds of his fanbase, restricting his creative freedom and eventually forcing him to give in to the demands of the masses. But what evidence is there that Kojima hated Metal Gear Solid 4 and didn't want to work on it?
Death Threats Are Awesome
Well, first of all let's look at his stated motivation for leading the project. This is from CVG, Nov 25, 2005:
Speaking about why he decided to head the latest MGS game, Kojima revealed that he received a number of death threats (not from CVG) after announcing that he would be less involved in the project. "The staff heard about this and got very nervous," said Kojima. "We talk today as if it was a joke, but at the time, it was not a joke at all. It was serious."
He seriously thought somebody was going to try to kill him! Or rather, multiple people. That can't be good for your feelings towards the game you're working on, can it? But that's not all. He didn't want to even make a sequel to Sons of Liberty in the first place, because it was a postmodern experiment that wasn't supposed to make sense! That's why he went into the past with MGS3, and tried to hand the project to his team repeatedly. But no, there was no avoiding it in the end: he had to swallow the bitter pill and pretend that MGS2 was supposed to be real, knowing that it would be a painful and unsatisfying experience.
However, he wasn't going to suffer silently...
Teasers Are Funny
Take a look at this comical teaser from 2005. Clearly there are tons of metaphors going on here, but most people were too busy kissing Kojima's ass and hyping themselves up for MGS4 to notice or care.
Naked Snake obviously represents Kojima, whose hiding place is blown up with the question "No Place to Hide?" representing his inability to avoid making a sequel to MGS2. He is then chased into Kojima Productions, where he is told to stop while everyone else takes their chosen 
places. Soon he realizes he needs to pick a spot before they're all taken, but he's always too late. When all the seats are full, we read "No Place for Hideo?", "No Hideout?" He then solves the problem by shooting everyone, and taking his seat as the designer, director and producer to much applause. Hooray! The "crowd" cheers as Kojima takes his seat.
But while this is going on, we see this picture of the director's chair belonging to one "Alan Smithee". For those who don't know, Alan Smithee is the official pseudonym used by film directors who want to disown a project! It may be nonsense or a tongue-in-cheek joke to most, but looking at it now, this was undoubtedly Kojima's way of letting fans of the story know that he wants to disown the project and simply couldn't. He had to keep his name on the product and own up to it.
After Kojima is seated and the epic music fades, Naked Snake takes off his mask and reveals himself to be Raiden! He winks at the camera as the fans boo him. Kojima has never forgotten the backlash towards Raiden and MGS2, and has since mocked Raiden with characters like Raikov and the Metal Gear Raiden: Snake Eraser video.
"No place for Snake?" it says. It seems that the unmasking of Naked Snake was to raise suspicions that Raiden would once again be the main character, but considering that Snake has represented Kojima until this point, it may also be a hint that Kojima is secretly still loyal to Sons of Liberty and his controversial decisions for it.
In any case, the rest of the video is a battle between Raiden and Snake for the Main Character chair, resulting in Snake's victory, to much applause.
This teaser, along with the subsequent Metal Gear Raiden video, proves that Kojima was having a dysfunctional relationship with the series and his fanbase at the time of MGS4's development, largely thanks to people's resentment of Raiden and his MGS2 experiment.
Quotes Are Amusing
In another interview with CVG that came out in 2006, after the first MGS4 trailer, Kojima openly admits that he didn't want to be working on the game:
"As a game designer, I'm very interested in creating something for the Wii. I'd like to run away from MGS 4 creation and create something for the Wii but unfortunately, I don't have anything that I can announce at the moment."
Kojima went around saying that Snake was going to die in MGS4, while also saying that Old Snake reflected his own feelings, about getting older and feeling older. But when we take all the pre-release quotes together, it becomes obvious that Old Snake was about more than simply aging — it was about feeling out of place, tired, grumpy, uninterested and worn out when it came to making the game.
"Once again I'd intended for MGS3 to wrap up the series, but so many people wanted to know what happened after "2". Things like the identity of the Patriots and so forth. I had planned on leaving those mysteries as mysteries, but people weren't convinced that the series was wrapped up.
"So ultimately we ended up making '4'. When work started on it, though, I began to wonder if my message of what we should pass on to future generations had truly gotten through, both to players and my team. After all, I've been conscious of the fact that this really is going to be my final Metal Gear, which means the team is going to have to continue the series themselves after I step away." (source)
Watching this interview (at 30:48) we read Kojima say about Snake's suicide scene in the trailer, "...The hidden theme here is that I want Snake to die so that I can move on." Clearly he was not enjoying the experience.
And here's the official Konami MGS4 website, where Kojima is being interviewed:
Q: Would you say Old Snake has the same mindset as yourself?
A: Yeah, I'd say he does. We're both old but we both think we have nice asses for our age (laughs).
Funny! Except we see how miserable and jaded Old Snake is with his mission before he even begins, and it only gets worse from there. I plan to do a deeper analysis of this later on, but suffice it to say that insightful fans could have learned from this that MGS4 would be a labour of obligation, not love.
Making Snake into a neutral factor in an arbitrary war is just as important when looking at the mentality of Kojima. In the past, every conflict Snake was in was meaningful, but as Kojima explained, it has become Side A versus Side B, and Snake doesn't care about either one of them. He flops from one side to the other as it suits him, much like how Kojima took whatever side he had to in order to get his lousy task done. As he wrote for Old Snake, "I'm just an old killer... Hired to do some wetwork."
Did the game's quality (and therefore the "Saga") suffer because Kojima was forced to work on it against his will? Yes, it did. And as I will explain in future articles, Kojima wanted to make sure of it.
Back to MGS4
2005 Teaser: http://www.gametrailers.com/player/5992.html
Alan Smithee information: http://en.wikipedia.org/wiki/Alan_Smithee
Same mindset as Old Snake: http://www.konami.jp/mgs4/uk/interview/03.html
Wants Snake to die: http://gamevideos.1up.com/video/id/3855 (30:48)
Death threats: http://www.computerandvideogames.com/article.php?id=129696
Run away from MGS4: http://www.computerandvideogames.com/article.php?id=140020&site=psw
