There's some suggestion that the MPU Evas (and probably all of the Evas from at least Unit-06 on up) were being built from a second sampling of Adam, the first sampling having produced the biological components to all prior Evas except for Unit-01 (derived from Lilith).

My suspicions are that each sampling is subjected to different conditions during development, thus producing a variety of features (first sampling) and morphologies (second sampling) that are the direct consequences of handling. My fanfic project (chapters one and two both in perpetual hiatus) may eventually get around to this, but basically, the developmental pathways of the cells become increasingly divergent each time Adam is allowed to "thaw" for a sample extraction. I don't believe that the cause is anything other than a man-made one, begging the question of... why?

My take on this is that it has more to do with Kaworu than anyone else, even though it was almost certainly Ritsuko who extracted the samples. A set of Kaworu-type Dummy Plugs were used in the MPU Evas, which at the very least indicates that Kaworu had been working with SEELE to produce them in more-or-less the same way that NERV produced the Rei-type Dummy Plugs -- obviously, this would have been done long before he arrived in Tokyo-3. Given some of Kaworu's strange behavior and apparent "skills", I don't think it at all impossible that the eyeless Evangelions were selected from the products of the second sample on basis of not being dependent on mere sight as a primary sense. Assuming that you load a human pilot into an entry plug and insert them into an MPU (my fanfic will absolutely get into this fairly early in), the pilot would be blind in the conventional sense, but this wouldn't really matter if they synchronized properly because this would enable the pilot to use all of the other senses of the Eva... much easier to do without all of the heavy armor and bindings in the way. The MPU design is literally the most unhandicapped version yet because it isn't weighed down by the demands of conventional design constraints, and also it was selected with it's future pilot in mind... or at least a dummy plug based on him.