According to evolutionary psychologists as well as the cultural main stream, men are going for sensually attractive women, while women are going for men who can provide them safety (plus other things we don't need to get into here). Whereas we might think that modern, cultured people are somewhat above those basic instincts and actually look for mates which fit their individual character, values, preferences, and interests, the world of online dating seems to throw us back a couple of centuries of progress. Many dating sites have been designed to increase usage and interaction with the site (so that more ads can be shown) and do this by relying a lot on pictures of their users to incite other users' interest. On the other hand, our individual character, values, preferences, and interests (or, ICVPI, for short) are to a large extent represented in text form as either essays or predefined answers to predefined questions. Now, while the text contains a lot of the relevant information, it is severely disadvantaged by this site design. Not only do the pictures have a much higher salience, their presence also directly speaks to our impulses and emotions (or system one, for those who have read Kahneman's "Thinking fast and slow") which hinders the already somewhat harder processing of text by system two.
The result of this click-optimizing is that user's choices whom to contact are much more driven by pictures (and therefore, looks) than by other criteria. This leads to the destructive effect that visually attractive women are swamped in messages among which it is hard and tedious to chose ones to reply to, while the less attractive ones do not have enough choice to find men that match their individual preferences. In other words, the mutual matching between people who might fit each other is more sabotaged than helped by those picture-driven dating sites.
Now, as a basic rationalist I will of course question my motivations and ask myself if the run for beauty is really for my own best or if it is a learned behavior stemming from our (in this case arguably superficial) culture. If we leave aside the antiquated Freudian principle of "drive" and read psychologists like Rogers and Fromm, we might realize that hunting for beautiful mates is just one way among others for a man to boost his self-esteem, not necessarily a motivator in and of itself. Indeed, modern studies have shown that lasting self-esteem and deep happiness can be created best by exercising our strengths in a meaningful way. (For details and the studies see Seligman's "Authentic Happiness".) Following this argument, if I get my self-esteem and social recognition from (for example) writing awesome blog articles and helping lots of people at work, then this positive emotion will "buffer" (in Seligman's terms) against any judgmental looks and statements that I will be facing when going out with my awesome, but ugly, new girl friend. (Can you hear them saying "what? are you dating her?" in a raising voice that bounces back from the ceiling?)
To sum up, wouldn't it be the most rational thing to simply switch off pictures on the dating site (Firefox currently has AddOns for this, Chrome can do it natively, just type "block" in the search box on the settings page), thus keeping my impulsive system one at calm, write more thoughtful messages, and get more and better responses, both because I am writing to less message-swamped women and because my own messages are better. Then dating will be less like a meaningless competition, the resulting relationships are more profound, and I will find out that my friends are not actually prejudiced against ugly people and will not look down at me for making that choice. Just let go of my own prejudices and false beliefs and I win. Right?
In my estimation, it is very difficult to cultivate an atractiveness function that does not highly value physical appearance. If you can do it, I think you will have made one of the most potentially important (and utility-bearing) moves on the board.
From my observation, the novelty on sexual attraction tends to be high, and fade relatively quickly. In contrast, intellectual/emotional intimacy (and just generally enjoying your lover's company) can have a sustained (and even increasing) value over the course of many, many decades...as well as having a compounding effect on other areas of your partner's attractiveness in your eyes.
It sounds so cliche that I'm having a hard time typing it without rolling my eyes and making a sour face...but... when it comes to love, find your best friend. Minimize the concern over physical attraction for the sake of optimizing toward a more comprehensive overall criteria.
We are, after all, all on the slow train to Uglyville. (Even the really pretty ones.) You'd be wise (and rational) to enjoy your company during the ride by choosing a mate on much more than looks.