The creative writing professor I had in university believed that all characters should be ugly. She considered beauty to be hideously boring, cliched, overused as a trait and therefore completely dismissible.
There's no question that ugliness is easier to describe. Split lips, Neanderthalic foreheads, scrubby hair, humps, club foots and general scrawniness are easier to envision than aquiline noses and high cheekbones. If you want your readers to clearly remember a character, remove the character's eye. The only thing is, most of us are no more especially ugly than we are especially beautiful. I personally am not astoundingly attractive, but I have no distinguishing characteristics that would describe easily just how I am plain-looking. If I were to write that I had bad skin, or a bulbous nose, or that I have a pear-like build, these things would be true ... but not in the degree that as a reader you'd be likely to picture. My skin is only lightly pockmarked. My nose is only a little bit bulbous. My stocky build isn't quite like a pear.
How much better for writing, however, that we exascerbate characteristics like this in order to make our characters more memorable and profound. We are expected to exaggerate. Writing is, after all, lying. Moreover, the description of the father's gut in chapter three will only serve to give a greater sense of growth when the father realizes his failing as a human being in chapter nine, vowing to give up his self-indulgence.
The tendency to exaggerate does not work both ways, however, for my professor from long ago had a point. Writers tend to make their attractive people - especially women - unnaturally attractive, so that every female denizen of the home and workplace embodies sexual perfection. It is natural that writers write out their fantasies; without fantasy, most writing would never happen. If you want to be taken seriously, however, and if you want to be published out of the porn industry, you will tone down the physical descriptions.
All right, but why?
We are all well-aware of our shortcomings. We may enjoy watching porn for its attractive, immoral participants, or reading about rich, attractive people, but in a world where there is so much of it on tap, it tends to roll over us like a wave upon the sand, quickly rolling off and leaving no special impact. To dig into a character is to tear up the sand and destroy the perfect image that was there before. Personal struggle is unpleasant and it is ugly; even if your character is beautiful at the start of your story, if he or she is to have any depth at all, it will be necessary to tear down the facade and reveal the unpleasant, uncomfortable truths about living. Beautiful people eat, shit, suffer and die just like everyone else, and those are the things that truly concern us all.
I like attractive characters in my stories, but I don't feel they have to be outlandishly attractive to be noticed. I don't particularly like physically ugly people in my stories - but people who are emotionally or behaviourally ugly fascinate me to no end. To wrap this up, if you have found yourself writing characters without flaws, or if you save your uncomfortable motivations for your villains, you must educate yourself. The division of characters between villains and good guys is stuff for old timey serials, not for legitimate writing. We are all ugly. We are all motivated by things we would not feel comfortable revealing to the general public - writers and non-writers alike.
And that is precisely why writers should write about it. To enable others to read it, and relate to it, and grow from it.