It shoudl be noted that the whole conversations of "the I who exists in" happened "before" Everyone was combined into one being. As I said before, those conversations were akin to the scenes in the movie where the many Rei's go out & lower everyones AT fields. It was getting rid of the perception of individuality in everyone before combining them into one being. Proof, Instrumentality didn't begin until the end of ep 25, after those conversations.
Again, it's not that humanity was reduced into imaginary friends, it's that humanity was reduced into Shinji, with no one else "real" to interact with period. Mind you Seele didn't likely intend for him to become the dominant ego, it was Lilith/Kaworu/Rei that decided that, and left him with the ultimate decision in the matter.
Rei/Lilith/Kowaru/God (whatever you choose to call it) deemed him worthy of choosing, Plus he was the Pilot of Unit-01.