This is something that ended up getting cut out of a longer Lost article (appearing elsewhere in the near future) rather early in the writing process. Clearly, it made no sense to disrupt a discussion of the many ways in which the show was stagnating for a thousand words about shipping, but somehow the idea has grabbed hold of me. Hope you don't mind leftovers.
To begin with, I want to be clear that when I call Charlie/Claire the best ship on Lost, I don't mean that they're the most romantic or the most sexy, that their attraction is the most believable, that the writers are treating the relationship well, or that I see a future for the two characters. No, I like Charlie and Claire because, unlike every other romantic pairing on the show, they interest me. I long ago stopped caring about the Sawyer-Kate-Jack love triangle (gosh! A pretty girl has to choose between a clean-cut good guy and a no-good rebel! How original!), and I doubt the addition of Ana-Lucia to the mix is going to change that. No power on Earth could make me believe that Sayid loved Shannon, and besides, the bimbo's dead (which hopefully means that Sayid can be an interesting character again). Sun and Jin are incredibly sweet, not to mention pretty, but they're done--they've overcome their problems and been reunited. Whatever comes next for them, we probably won't be seeing it on a Disney-owned channel. Same with Rose and Bernard. Charlie and Claire are the only couple on the island whose problems remain tangled and realistic, which is why it sucks (in a way emblematic of how the entire show has come to suck) that in nine episodes their relationship got maybe ten minutes of airplay, as opposed to endless repetitions of Kate vacillating between Cyclops and Wolverine and Sun gazing longingly at the horizon.
It's not that I'm so fond of Charlie and Claire as characters, either. He was quite sympathetic for a while there in the show's first season, but lately he's become judgmental and priggish. Claire is barely even a character--beyond a few details, we have no idea who she is. Which is part of what makes the relationship between her and Charlie so interesting--neither does he. Without ever acknowledging that they were doing so, Charlie and Claire skipped right past courtship, dating, romance and marriage and started playing house. They don't know each other. They don't love each other. It's open to debate whether they're even attracted to each other (the closest they've come to intimate contact is Charlie kissing Claire on the forehead). They're deeply invested in each other, but for reasons that have very little to do with who the other person in the relationship is.
Like, I suspect, many drug addicts, Charlie is a control freak. That desire for control doesn't express itself through an anal attention to detail, or a desire to dominate those close to him (although he skates rather close to the latter with some of his actions towards Claire). Charlie feels in control when he's taking care of others. He needs to be the man of the house, providing for and protecting his family. The kind of person, after all, who is capable of taking care of others surely doesn't need to be helped himself? In other words, Charlie is trying to fake it till he makes it, using other people as props. We saw last season how a previous attempt of this kind failed disastrously, but a combination of fortuitous circumstances has given Charlie a second, more promising chance on the island. I won't pretend that it doesn't speak well of Charlie that he was the person who stepped up to take care of Claire--assuring her that "[he's] not afraid of [her]"--early in the first season, but the fact remains that Charlie is using Claire as a way to avoid his problems, and that way lies only pain for both of them.
For better or worse, Charlie is the sort of person who will justify almost any action if it benefits the people he cares about--or, more accurately, the people he cares for. He'll bully Hurley shamelessly ("You're going to lie to the baby?", "I thought you were my friend!") to get Clare a favorite dish. He'll ignore Danielle Rousseau's obvious emotional distress because she endangered his family. And, most famously, he'll kill a man in cold blood and justify it by saying that he was protecting Clare. It's not the worst way to be, I suppose--there is some mileage to be gained in taking care of your own--but given that Claire and Aaron aren't Charlie's own, or at least that the relationship between the three hasn't been formally discussed, it's an attitude fraught with the possibility of conflict.
Claire, for her part, has obvious reasons for latching onto Charlie. I don't want to say that she went looking for a daddy, but whether consciously or not, there was a point in their burgeoning friendship in which she accepted his unspoken offer of shared responsibility for her child. That she is now second-guessing herself, as we learn when we see her speak to Locke in "Abandoned", is only natural. The fact is, however, that if Charlie and Claire were a normal couple, if they had met, fallen in love, gotten married, and had a baby in that order, they would still be having trouble right now. Babies put a strain on relationships. The sniping the two exchange earlier in "Abandoned", when Charlie points out that Claire shouldn't have woken the baby (or run with him towards Shannon's screams) is probably familiar to thousands of new or formerly-new parents, and it is somewhat disingenuous to claim, as many fans have done, that Charlie had no right to grow annoyed with Claire because he isn't the baby's father. She had no problem, up until that point, with letting him take on a father's responsibility, and it does follow that he has the right to act like one even when it doesn't suit her.
The problem is that unlike those other new parents, Charlie and Claire have no bedrock of genuine feeling to fall back on. So, we get Claire making vague overtures towards Locke as a possible replacement for Charlie, and Charlie making horribly inappropriate judgments about Claire's fitness as a mother. The relationship is clearly going to go sour, but unlike other instances of romantic tension that we've seen on the show, it might do so in an interesting way. There's so much potential for disaster here--two well-intentioned, damaged people facing up to the consequences of acting without thinking about the consequences. We could see fights, we could see Claire kicking Charlie out and Charlie trying to take Aaron. We could see Locke getting caught in the middle (and isn't it a blast to watch Mr. Cool start sweating the minute he's placed between those two?). And we could see actual love, because when it comes down to it, Charlie and Claire have potential. They suit each other. They're comfortable together. They want their relationship to work. Twisted as it is, this fledgling romance could yield something real--and it'll be a long, rocky road getting there.
Which is why I despise the drug twist. Charlie falling off the wagon is the equivalent of finishing off a delicate stone-carving with a ten-pound hammer. The very real problems inherent in the relationship will cease to matter, overwhelmed by the simple fact that Charlie can no longer function as a husband and father (I'm envisioning Charlie blissing out as Aaron plays at the edge of a cliff, or something similarly melodramatic). If he doesn't, the fact that he might--that he's still carrying around that unopened Virgin Mary statue--will constantly be on our mind, informing and tainting every conversation between the two. There's enough baggage and issues plaguing this relationship already, and an unsubtle trick like dangling a plane full of heroin before Charlie does nothing but bleed an interesting character dynamic dry.
Which is probably what the writers want. As I mentioned above, they haven't exactly given Charlie and Claire a great deal of air time over the second season's first half, and in general the episodes we've seen have demonstrated a preference for simplistic storytelling--the whole 'faith vs. science' dilemma is a good example. I suspect the best we can hope for from Charlie and Claire is Charlie getting back on the horse in time for February sweeps. The writers probably don't expect us to care--after all, we'll be too busy watching Jack choose between Kate and Ana-Lucia.