In "Brave New World," can John be compared to someone who is unable to orientate himself because his ideas are incompatible with reality?

That John is an anachronism in the New World is clear.  However, he cannot orientate himself to the world of Lenina and the others because their world is a false world.

The character of John the savage in "Brave New World" acts as a foil to the other characters who lack what makes people truly human.  True, his concept of love between a man and woman is certainly idealized from his reading of Shakespeare; yet his love for his mother is of the genuine kind.  His human grief when Linda dies is in sharp contrast to the reactions of the Delta children, pointing to the hideous dehumanization of the creatures of the New World. 

It is the inhabitants of the New World who are incompatible with reality, not John.  For, although he at first has been enthralled by Lenina's beauty and the surroundings which cause him in awe to remark, " How beauteous mankind is! O brave new world!" at the hospital where Linda dies

He halted and, with bewildered and horrified eyes, stared round him at the khaki mob, in the midst of which, overtopping it by a full head, he stood, 'How many goodly creature are there here!' The singing words mocked him derisively, 'How beauteous mankind is! O brave new world...'

The character of John is clearly the vehicle of satire for Orwell, a character who, as a foil, points to the dysutopian characteristics of the New World created to eliminate wars and disastifaction.

Sadly, John's character is not unlike people who have values and find themselves in an environment in which these values have been villified.  They, then, are incompatible only because the world into which they have been placed is false, the "reality" an unreality, in fact.