Replace the entire Nerv bridge crew with the bridge crew from Star Trek TOS:
Gendo = James Tiberius Kirk
Fuyutsuki = Mr. Spok
Dr. Akagi = Leonard McCoy
Maya = Uhura
Hyuuga = Sulu
Aoba = Chekov
Kaji = Mr. Scott
Misato = ? I dunno who'd replace Misato aside from Kirk. Maybe leave her where she is.
Seriously, what is wrong with you guys that you haven't suggested this yet? And if it has, then my apologies. I must have missed something.
Edit: How on earth did I manage to misspell "Spock?" I guess typing stream of consciousness has its disadvantages.
I keep wondering if The Doctor has been suggested yet. Probably.
I also wonder about Integra Hellsing taking over Nerv...or at least showing up to have a staring contest with Commander Ikari, complete with scary glints of glasses.
"Well Misato your proton particle beam cannon looks pretty good, but I think we all know what it needs."
Misato sighed and glanced back at the head of Nerv. "More power sir."
"You're darn right more power!".
After the battle it was generally decided (by those who survived) that attempting to use the S2 engine recovered from the 2nd angel to power the cannon had been a mistake.
Gendo = Tim
Fuyutsuki = Al
Dr. Akagi = Wilson Wilson, Jr
Maya = Heidi Keppert
Misato = Jill Taylor
Though technically, Schultz know more about what's really going on in that Stallag than any of the other Germans there. He just habitually disavows knowing anything.