Creator Backlash: Done to Raiden from the previous game. Zero devotes a long CALL to the fact that the Raiden mask irritates him, and the Raiden mask is used to pose as Raikov, the impulsive, despised and ill-tempered lover of everyone's favourite homicidal lunatic Volgin; Snake beats him up and hides him in a locker, with the option of actually killing him. This pleased Raiden's substantial Hate Dom no end. He got better.
In the Secret Theater video "Metal Gear Raiden: Snake Eraser", Raiden goes back in time to assassinate Naked Snake/Big Boss and take the Main Character Chair for himself. He ends up, among other things, getting kicked in the face by Naked Snake during the HALO jump, and almost raped by Volgin, mistaking Raiden for Raikov.
The Metal Gear Solid 4 trailer also takes a potshot at Raiden, with the crowd booing heavily when he unmasks himself and his getting royally creamed by Snake during their fight for the main character chair.
Fake Nationality: British-born Neil Ross and American-borns Jim Ward and Grant Albercht voiced Russians.
Screwed by the Lawyers: Why the Snake Vs. Monkey mini-game isn't in the 3DS and HD versions. Sony Computer Entertainment created, and owns the rights to Ape Escape, killing any chance the mini-game has of being on other consoles by default (though it doesn't quite explain its absence in the PS3 and Vita versions).
There's also plenty of made up plants and animals: For example, there's no such thing as a Baltic Hornet (hornets can't make honey) and there is no golova fruit (although, it's based off of a real fruit called a jackfruit).
Artistic License - Geography: Good luck finding any tropical jungles anywhere in the former Soviet Union, not to mention the ludicrous variety of animals housed in it. The justification is that the animals were brought into the jungle from other regions by the scientists for research purposes, and the jungle setting is there mostly to trick people playing the pre-release demo.
Despite the game saying it's a "jungle", it looks more like what's called a mixed forest, which the Soviet Union did have, for instance the Caspian Hyrcanian zone in Azerbaijan. Also, there actually are pockets of lush forest right next to arid mountain regions in areas of Tajikistan (where the game is suggested to take place) like the Varzob region. The mountainous areas later in the game also resemble the lower ranges of the Tian Shan mountains in Krygyzistan.
Artistic License - Economics: The Philosopher's Legacy consists of enough money to fight the Second World War five times over. The economic repercussions of putting this much money aside and doing little with it, then losing it... Although the next game actually does deal with the economic repercussions somewhat.