What has boggled my mind is that Kojima is about the only Japanese guy to make a game with story and is about the only talented one from that whole country. The rest of them only seem to produce button mashers, stupid anime games and poorly executed fantastical hack and slash pointlessness that all feature weird yelling and whining child like sounds.
Kojima is probably hated because he can actually make a great game with a great story and gameplay.
I've always loved Japanese games.

Their best games are much more beautiful and have "tighter" mechanics.
The latter point is a little hard to describe without examples. The main one that sticks out in my mind: health systems. Many Japanese games don't feature health bars, or have very small health bars. You aren't supposed to get hit in these games; taking damage is almost never necessary. Many players master the levels, and then clear them "perfectly". In contrast, Western games have never been like this. They've always featured big health bars and ample health replenishment. Taking damage is inevitable.
While I'm not going to argue which style is inherently better, I prefer the Japanese style. When the player must be able to clear a stage without taking damage, every aspect of the game must be carefully considered. When you have a huge health bar and the environment is littered with health packs, the developers can get away with much sloppier design.
Have you ever tried the Souls series (Demon's Souls, Dark Souls I/II, Bloodborne)? These are modern "action RPGs" with a subtle method of storytelling. There are few cutscenes or dialogs, but the "story" is told through visual details and item descriptions. You have to piece the story together on your own, and doing so is quite fun. The attention to detail is meticulous.
Anyway, I mention these games because they have almost no anime trappings and show the strengths of traditional Japanese game design in an era where, sadly, many Japanese developers seem to have lost their way.
Some great Japanese developers:
Platinum games (hideki kamiya, formerly shinji mikami)
Nintendo (at times... I wouldn't call them too great these days: Shigeru Miyamoto, Yokoi Gunpei (RIP))
FROM software (hidetaka miyazaki)
CAVE
Capcom (many... most gone now. studio has had its ups and downs over the years)
SCE Japan Studio (Fumito Ueda -- departed now)