Intrapapillary? I am sorry but that makes absolutely no sense. It is possible that he/she said interpupillary distance, but that would not have any effect on lasik.
Small eyes? If your doctor mentioned that your eyes are too small, he/she may also have meant that your eyelids do not open wide enough to allow the suction device used to help create the lasik flaps sit properly on your eye. You may want to seek a second opinion as there may be different options available to you.
LASIK. He is probably concerned about the distance between your eyes, also called the intrapupillary distance-- if it is too close together, he may be concerned that your eyes are not lined up properly or that positioning may be difficult in the laser room. If he is using the intralase to create the flap, your eye may be too close to the nose to create a good flap.
Difficult to say. Interpupillary distance has nothing to do with lasik candidacy. I would get a second opinion.