I have played 40+ hours and have a few tips for manual rating:
1. Rate consistently. Try as much as possible to rate the same features the same as you rated them on the previous model. If you can remember how you rated the previous girl, the system will learn your preferences faster.
2. Some points should be given for features that are closer to your ideal, even if they're not perfect. For example, I want a smaller thigh gap, and model A has a larger gap than model B, even though both are far too big. In this scenario I might rate model A 0 or 1, and model B 2. Similarly for personality, if the girl does not immediately get mad and leave, she deserves at least 1-2 points for anger management. This is how you avoid models who immediately get pissed.
3. It's very important to go through all the dialogues/photographing for each model, especially at the beginning. Some models will only react to touching a certain spot, or will only be willing to undress after a certain affection level (green bar) is reached. So you should try to get the affection bar as high as possible with each model via dialogue options and photographing. Otherwise, you will not be able to accurately rate personality traits.
4. Sometimes you simply will not be able to rate a certain trait, for example a girl with a long skirt who refuses to undress you can't rate the crotch, since you can't see it. In these instances I prefer to rate 5 since this is a neutral rating, whereas zero will categorically reduce the trait from the gene pool. Or you can use Monkey to remove clothes.
To me, half the fun of the game is taking time with the manual ratings and seeing what the system will spit out next. I encourage everyone to give it a shot at carefully rating through a few levels and playing the game as it is meant to be played, as it is quite fun that way.