I wonder how many of those pictures were taken by him.
Sue Lyons has the property that it is almost impossible to take a bad picture of her. I'm sure that's one of the things that made Kubrick hire her.
According to Wikipedia, Tuesday Weld was considered for the part. She also has that quality - she's delightful from pretty much any angle, with any expression on her face, and wearing anything.
Perhaps she was too well known, and therefore too expensive. Also, I think Kubrick wanted someone unknown, an new face. By 1962, Ms. Weld was already very familiar, having appeared in nine movies by that time. Also, she's three years older than Sue Lyons, and probably wouldn't have been able to pull off the "precocious 14-year-old" thing by then.
Sue Lyons not only had the photographic quality that you describe so well, but she was 13- and in the book Lolita is 12 1/2. An inspired choice by Kubrick.
Poor Sue Lyons sure went on to live a screwed up life afterwards.