It's rather tempting to write Aylmer off a big old jerk. Let's consider his character for a moment, in slightly modernized terms: he's unhappy with his beautiful wife because she's just not hot enough. He tells her as much, and then practically insists that she get plastic surgery. When he realizes such a procedure is terribly dangerous, he goes forward with it anyway, and ends up killing her in an attempt to make her perfect. Not exactly an ideal husband.
Yet both Aylmer and Georgiana make every rationalization for this behavior. Aylmer reasons that the birthmark is Nature's way of showing Georgiana's mortality and necessary humanity. He wants to remove the mark, then, not because he doesn't like the way she looks, but because of what the symbol represents to him (see "Symbols, Imagery, Allegory"). He's not actually the shallow fellow he appears to be. Georgiana later reasons that his love is all the more noble for its desire to make her into something perfect. Aylmer is not satisfied with an earthly, ordinary love – he dreams of something greater.
Of course, it is just this something greater that really gets out Aylmer into trouble. We've got him off the hook for superficiality, but we still have to deal with his big character flaw: ambition. Actually, make that foolish ambition. Aylmer seeks to unfold the secrets of the natural world, and not only know the mechanism of its power, but in fact harness it and become a creator himself. In short, he's guilty of what Hawthorne sees as two problems in the scientific world around him: the desire to play God, and a blinding faith in science.
We know these things about Aylmer from the beginning of the story: that his love for science rivals his love for Georgiana, and he has devoted his entire life to scientific inquiry. Because of his nature, we can look to these two "flaws" – the desire to play God and a blinding faith in science – as a strong contender for the reason behind Aylmer's obsession with removing his wife's birthmark. You could even argue that, as much as he cares about making his wife perfect, he cares at least as much about the science behind the process, and the prospect of rivaling nature with his own scientific abilities.