I guess Shinji's base attraction to Rei was Her resemblance to Yui. To feel that motherly warmth from a significant other's perspective would be a gift. A mother more motherly than your own mother yet with the face of your mother. Surpassing yet being equal to that position. Rei is a hybrid between Yui and Lilith. The "raw" Lilith was the one we saw below the NERV HQ. And I guess Rei's "attraction" towards Shinji is obviously from Yui's DNA. Rei being "man-made" proves that there is a natural way of Third Impact. What we saw was human initiated.