I'm going to confess it - I like my unpopular stories better than my popular ones. It's not like I dislike them getting popular, not at all. I feel satisfied that Inamorata as 1.8 million reads, and I'm tickled pink that The Child's Father and Three Anniversaries have done fairly well for themselves. Though I want to throw up every time I see The Cabin Boy, Lifelines, and the The Child's Father series, it's nothing to do with their relative popularity (keep in mind, this is RELATIVE popularity. Ain't nothin' so popular as Inamorata, and I have literally no idea why).
So why do I like unpopular stories? Good question!
I like my unpopular stories better than my popular ones because of the freedom I have with them. For example, I could kill Dr. Stephen Byrne - from my wildly unpopular story The Storm-Grey Sea - in the next chapter and I wouldn't hear a squeak from anyone. I could also decide that, fuck this relationship of Stephen/Rosalind I'm setting up, I'm going to start shipping (aha, a wild pun appears!) Stephen/Vice-Admiral Marlowe instead.
Or Stephen/his surgical tools.
The possibilities abound, really. But with Inamorata, the moment it started to get popular, I lost that freedom. I was quite at my liberty to chuck major character death and unconventional relationships around like confetti before I got featured. I was also able to spend four pages describing a book if I damn well pleased. Now, I love that I was featured, but the moment that happened, along came this whole idea of making my story not too shocking. I had a responsibility to write well and to please everyone. In fact, Nightingale's eventual romance with Robin was too much for a lot of people (see: "lol shit characters shit ending great story", or something to that effect, a comment I received on Inamorata that will eventually be carved on my tombstone for how much I love it).
So with my shockingly unpopular The Storm-Grey Sea and The Fires of Spring (both being two of my favourite things I have EVER written), I've got more freedom. I can freely write about Christopher's sexual debauchery, and spend an obscenely long time lovingly describing a forty-two pound carronade.
Don't take this the wrong way, as I'd love to have all my stories at the top of all the lists, and I hate it when popular authors bitch about their popularity (I love my fans, seriously, I LOVE YOU GUYS), but I'm just pointing out the level of freedom and lack of responsibility that comes along with an unpopular story.
So if you have an unpopular story, work it. Love it. Do whatever you want with it. Buy it dinner, take it home, and then make sweet, sweet love to it. After all, it's your story, and no one can tell you what to do with it.