Hyuga, in the co-pilot's seat, with Misato and Shinji in the foreground.
MISATO (BACK):“Withdraw immediately once you've released the Eva.
Ascend until you reach a safe altitude.”
UrsusArctos: Yet another instance of "the main characters do everything". Hyuga being qualified to sit in the pilot's seat is a bit of a stretch - they could've gotten a nameless pilot to follow Misato's orders just as well.
imprimatur13: Obviously, what happened is, they put out a notice on the NERV PA system: "We need someone to pilot the transporter to pick up Captain Katsuragi. Any-"
Hyuga: "I'll do it."
Maya: "But you don't know how to fly a plane!"
Hyuga: "Maya, there comes a time in every man's life when he must do the impossible, disregarding all thoughts of personal safety. That time, is now."
singing quietly to himself: "Do the impossible, see the invisible; Row Row, fight the power..."
ath: To be fair, the scripts says he's sitting in the co-pilot's seat. Note that he's actually sitting in the left seat, which in reality is the captain's seat in virtually every fixed-wing aircraft. Right-hand-drive confusion on part of the storyboarder, I guess...
imprimatur13: Well, I see your point... Counterpoint! Misato tells Hyuga to withdraw the transporter, not the pilot (whom we don't actually see at all; and who, for all we know, isn't even there). Apparently, he is expected to know how to pilot it on his own. Somehow.