8. Olga Gurlukovich Doesn't Shave Her Armpits (MGS2)
The first boss battle in MGS2 was against a female Russian commando with a pixie haircut. I thought she was actually kind of cute, until Snake made her put her hands up; this revealed two hairy armpits staring Snake right in the face. It's a minor detail, but when you think about the fact that someone made the decision to purposefully give her two underarm afros, you realise how weird it is.
7. Naomi Lost Her British Accent (MGS4)
Just like Mei Ling, it's a simple retcon; in MGS1, Naomi had a distinct British accent, which she largely seems to have lost by the time MGS4 takes place.
6. Raiden Is Named After A Disposable Japanese Aircraft
Jack's codename "Raiden" was named after an attack aircraft that was cheap to manufacture and maintain. This is because he was put through the entire Big Shell experiment by The Patriots as a way for them to test just how easily people can be manipulated. That's kind of a downer, but luckily "raiden" also means "lightning" in Japanese, so we'll pretend that's what he's really named after.