NeoEliteShipping (Lance/Karen) -- One of the reasons why I love this ship is chemistry. I feel like they would have lots of it because they're so different from the way they come off, but also similar. They're both cool, but I see Lance being heroic and Karen being...anti-heroic? lol! Opposites attract. xD I don't see too many fanfics or fanart about them, so I guess this is a rare ship!
SpiritShipping (Morty/Jasmine) -- Really, I've only seen like...one fanart of this ship and it makes me sad. Granted, I like this as an unrequited ship, but I still think it's cute! I have headcanon that Morty and Jasmine were actually childhood friends, but that's another story. :P
SteelCareShipping (Steven/Jasmine) -- Yessss, oh my gosh, I think this one is really cute, but I also feel like people hate it. >_< I have headcanon for this too where Steven and Jasmine are actually acquainted long before Jasmine became a Gym Leader and Steven was still a brand new Champion. Jasmine would obviously look up to Steven as a Steel-type Trainer role model and maybe even have a celebrity crush on him.
Like ever other girl.
I've seen like two fanart of them together (by themselves) and I've read maybe 3 fanfics on them... *cries in a corner*
SunnyShipping (Flint/Jasmine) -- Yes, I know, I ship Jasmine around a lot, but this one even has canon context in the anime (unlike Volkner/Jasmine which I love) and yet, it's not remembered much. xD Flint would be such a sweetheart on Jasmine and Jasmine in turn would admire Flint's passion. I just love them either as friends or more.
RockSmashShipping (Brawly/Roxanne) -- This one is one of my more recent ships, but I'm surprised there isn't much shipping for it considering it's a little old (then again, Brawly and Roxanne didn't have much personality back then). I thought for sure ORAS would have bumped this shipping, and it did by getting noticed, but I don't really see much fanworks on it. I'm probably just not looking, but I still consider this a rare ship.
FleurdeGrenadeShipping (Grant/Viola) -- Ever since they appeared together in that one XY episode, I fell in love with this ship. Grant and Viola act like such good friends, I couldn't not
ship them. xD I can understand why there isn't much fanworks on them together since they only appeared together once, but I don't care. This is probably one of my favorite XY Gym Leader ships.
LaserBladeShipping (Clemont/Korrina) -- Love this one too!
I know it has it's own thread outside this one, but it's still not getting much activity, sooo...rare ship? I think so ! I've only seen a few fanart of them and even fewer fanfics, and that's sad because I really think they're cute together. Plus, I kind of like the fact that Korrina's probably a little older than Clemont. He would be trying to impress her in some ways, but Korrina would maybe be oblivious to that and only find Clemont as a cute little brother. xD
ElectricBounceShipping (Clemont/Shauna) -- I thought it was kind of random that Shauna, in the game, mentioned how she was friends with Clemont and Bonnie, but there wasn't much more than word of mouth. I'm hoping that with the third XY game (if it comes out) that they expand on this a bit because it's adorable. It's almost like Clemont/Korrina, but Shauna being closer in age to Clemont. And Shauna's already close friends with Bonnie, so that's a plus right?
SnazzyShipping (Lucian/Cynthia) -- If I'm not shipping Cynthia with Steven, then I ship her with Lucian. They'd be a badass couple imo...and amazingly fashionable at that. Haha. I ended up really liking this ship due to a fanfic author I'm following on FFNet; she makes their relationship so awesome. <3 I feel like this is a rare ship, but I could be wrong. lol
BoilingWaterShipping (Siebold/Malva) -- Again, I might be looking in all the wrong places, but I feel like this one isn't very popular aside from the amazing fanart I occasionally see. I just love the fact that Siebold and Malva would have a love/hate relationship. They're...hot together. *shot*
Valerie/Anyone! -- I don't see Valerie being shipped around a lot (unless she's with Siebold and/or Grant). Haven't found my favorite Valerie ship, but I'm leaning towards MidsummerNightsShipping (Wikstrom/Valerie) or even VestalShipping (Valerie/Viola). Valerie has a great design and I'd love to see her getting shipped more with other characters.