Turns out Second Impact caused a Shadowrun style Awakening, which leads various corproate and government groups having an interest in Nerv.
First up
Harlequin who has actually been in and out of Shinji's life ever since Gendo dumped the poor lad. Shinji views him as an eccentric Uncle figure and is always happy to see him. Harlequin has been protecting the boy since various powers aren't fooled by Gendo's disinterest and seek to manipulate the youth to their own ends.
Next
Dunkelzahn the current President of the UCAS providing politcal support, and then there's
Lofwyr who has provided a lot of Money to Nerv and aside from the right to inspect the results of his investment, took Asuka under his wing after the tragic death of her mother.
The great Dragons support Nerv and it's mission, afterall it prevents them from having to fight the Angels. However none of them are thrilled with the idea of keeping teh Eva's around once they've outlived their usefullness, and are of course plotting Nerv and Seele's downfall. To that end two supposedly dead great Dragons have infilitrated Nerv itself.
Nachtmeister is the head of Nerv logistics and finance under the name Nicolas Masters. He's the one that makes sure the lights stay on, the personnel are paid, and that Nervs books are always in the black.
Feuerschwinge runs Nerv's security division under the name Fleur S. Schwinger, she's keeps a close eye on the unit responsible for protecting the pilots and employs Shadowrunners to eliminate threats to Nerve (and her own) interests.