All right guys, I don't mean to go back to television (again!) but I need to for an example: Have you ever watched a TV show where the OTP doesn't have as much chemistry as another pairing? I feel like there are two types of people: those who follow canon no matter what (because it's canon) and those who side with chemistry, whether it's canon or not.
I'm one of the latter people.
It's frustrating to hear that canon wins because canon is true. It's even more frustrating when the canon couple has absolutely no chemistry - even if the acting and writing is good.
Chemistry sells a couple to me, whether in television, movies, and especially books. I've read books where I've been like, 'Why do you like this guy?' and I've read books where I had to fan myself off because the chemistry was just so smoking. (Great examples of chemistry? Hush Hush by Becca Fitzpatrick and Bloodlines by Richelle Mead.)
In a way, it's easier for us writers to infuse chemistry into our couples, with little glances, touches. The difficult part is trying not to force it, trying not to smack your reader over the head with a sign that says, "YOU MUST SHIP THIS PAIRING BECAUSE THIS IS WHAT IS TRUE." I guarantee that in nearly all cases, if you write good chemistry, they will ship that couple.
Television has it harder because they may not originally start out with a character's true OTP. Then, when they're writing one, they may pick an actor/actress without testing chemistry. A lot of the times, it's like: "Oh, well they're both good looking, it'll work." For that, I throw the BluRay of The Tourist at them. The two most beautiful people in the world didn't have chemistry together (although, I maintain if Johnny Depp looked the way he did in Public Enemies, my screen would melt off because of the hotness). You can't expect to random actors to magically have chemistry just because they're supposed to be a couple.
Then we get to the other side of the coin. Television producers also don't expect when two characters (actors) who aren't OTP have chemistry. I absolutely hate when they're in denial about it (cough Penny and Sheldon cough). I love when the chemistry is so obvious that the writers have no choice but to write something in regards to it (cough Jeff and Annie cough).
Sometimes, as a writer, you intend for one couple to happen when the chemistry between your hero/heroine is stronger with someone else, and before you know it, they've already gotten together so when you try to change it and fix it, you can't because it feels wrong.
Go with it. These are the best stories to tell because you, the writer, don't even expect it. It's why nearly all my shipping isn't canon.
And if people ship your hero/heroine with someone else, let them. You can't fight chemistry.