After the honeymoon phase is when all the real thoughts begin to come out, when people start to think that pretending to be awesome in every respect is tiring, surreal, whatever. Usually it's when people start to question whether the relationship was ever 'real', like 'he's not who I thought he was'. 'She's different now'. The reality is, each person is getting to know the reality of their partner.
That's the point.
The honeymoon phase, IMO, is actually the worst part of the relationship, because it's founded on a lot of pretence in most cases. Whereas after it, there's actually so much to discover; the real person. The biggest issue people have with this, in my experience, is expectation. If you don't expect your partner to be perfect, and you're realistic about it, the transition between honeymoon phase and reality becomes a lot smoother.
One thing I also notice all the time in the dying embers of the honeymoon phase is this paradigm shift in the way two people relate. It becomes a lot more about 'me'. For instance, the woman might say 'I'm just not that excited for sex these days', or the guy might say 'I'm not really a guy who talks about what's on the inside'. What people seem to forget is that they are in a relationship where two people have needs. Understanding the other person makes a tremendous difference to the outcome of any situation.
Take the dwindling sex scenario, which is probably one of the biggest issues couples have coming out of the honeymoon phase. Recent studies suggest that men are more action orientated, and actually more inclined to get their emotional needs fulfilled from sex, than women are. This is because, as we know, most guys don't do a lot of physical touching, hugging, with people other than their partner. So sex, for guys, is actually pretty important in a relationship in terms of physical human contact and keeping up self esteem. One study reported that a guy who was rejected continually for sex by his partner gained weight, became anxious and agitated and generally depressed.
Now, to me it seems simple. It's a case of empathy. We know women are the more approached sex, and generally, in relationships, men tend to do the brunt of the coming-on-to-their-partner. But ladies, forget that you're all insanely attractive and your partners want to have sex with you every ten minutes, for just a moment. Imagine instead, that he came on to you maybe once a fortnight, and every other effort for sex was initiated by you, maybe three to five times a week. And every time, apart from your once a fortnight when he dictated 'we're having sex', you were rejected. Now add on top of that the fact that as a sex pressured to be strong and independent, you had little or no physical contact with anyone else at any point during those two sexless weeks, apart from the occasional handshake at work.
You wouldn't find it hard to understand why little sex is such an enormous issue for your partner, then.
Or say for instance that a guy doesn't open up to his partner. Studies show women generally have tremendous support systems in comparison to men, engage in lots of physical touching with people apart from their partner and so don't require the same level of physical intimacy as men, but women also tend to get their emotional needs in a relationship fulfilled in verbal communication, non-physical affection, talking about problems, venting to their partners etc. Where sex is more often a man's key to release and contentment, open communication is more often a woman's. So if a man doesn't speak to his partner, she may very well feel left in the dark. Without non-sexual, non-physical showing of affection, a woman will likely fall into the same depression a guy might when deprived of sex. And a guy, simply by putting himself in her shoes, understanding it, can give her what she needs.
The same thing goes with anything, on both sides. Empathy. Putting yourself in the other person's shoes and trying to understand why something is an issue. Too often people out of the honeymoon phase try to invalidate their partner's needs, don't make the effort to understand the situation fully or just want to continue pretending everything's rosy and awesome. But it's actually not that difficult to just have empathy and address the issue.