The cover story of 'Only post-2I Children' is kind of needed, since Units-00, -01, and -02 are all set by the facts of Rei I, and Yui & Kyoko's Contact Experiments make it so that Rei, Shinji, and Asuka have to be the first 3 Pilots. Once you've gotten that far, you need an explanation as to 'Hey, why are all your Pilots 14 year old kids?'. Once you've done that, it's easier to keep rolling, especially as #1) 14 year olds are easier to manipulate and #2) if you're Gendo and SEELE, you know there aren't actually going to be all that many Evas and Pilots. Even without the MP Dummy Plugs, they'd still have been able to fill out the numbers just from Class 2-A.