Looks like you need to listen to more CODEC conversations.
The Gekko's legs are left unarmored to reduce it's weight. According to Otacon, Gekkos are meant for indoor ops (wherever they can fit) and having armor on the legs would make it so heavy that it'll fall through the floor. Because of that, armor is only focused on where the brain is housed.
In Revengeance, a conversation with Doktor reveals that the Gekkos have improved leg armor due to the CNT technology. Meaning Raiden can't slice through them like he did in MGS4, unless he weakens them beforehand. --- There is no such thing as a "Quick Time Event done right". A game that has Quick Time Events is a "video game done wrong".