In an interview with IGN, Hideo Kojima talked about his favorite characters in the Metal Gear series.
The first should not be a surprise: Snake. This is the character closest to Kojima. He has been in every Metal Gear game since the beginning, and throughout the years his backstory grew.
Kojima also mentions Otacon. Even though he is not very heroic, like Snake, Kojima thinks his role in the series is very important. He also feels this is probably the most relatable character for those who play the Metal Gear games.
Kojima explained he always designs boss battles with two things in mind: how will the player fight them, and how will they fit into the story?
From Metal Gear Solid 1, Kojima likes Vulcan Raven a lot. He likes how the boss battle turned out. After being defeated by Snake, he still keeps standing, and never kneels down.
In Metal Gear Solid 1, you face ever stronger bosses as you progress, but then you come across Psycho Mantis, a skinny, ‘bondage’ character. You may first wonder how he is stronger than the others, but his power comes from his psychic abilities.
In Metal Gear Solid 3, the player faces The End, a legendary sniper. Kojima initially wanted the battle to last two weeks, but the staff advised against this idea.
In the same game, there was also The Sorrow. The fight against him was unique, because he was a ghost, a boss that did not exist, and the player has to defeat him by bringing himself back to life.
You can watch the entire interview for yourself below.
Source: IGN UK