The three I 'ship most strongly are Xianghua/Kilik (Ill fated, schmil schmated. I'm still pulling for those two crazy kids to get more than one lousy night together and a son neither of them got to raise), Siegfried/Hilde (I considered Hilde's ending in IV one of the ones I'd prefer most as canon before V was released, and I still think it's a good culmination of Siegfried's story to find someone that knows his past and accepts him anyway), and Viola/Z.W.E.I. (Just 'cause, really, but I like the jaded badass and the quiet girl type pairing.)
On to others that I've toyed with...
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: I liked Tira/Sophitia as a messed-up Foe Yay pairing, but Pyrrha's stockolm-tastic dependence on Tira as the only person who doesn't die horribly around her and Tira's possessive, twisted, extremely abusive but nonetheless apparently genuine affection for her makes for a fun dynamic.
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: I sort of imagine this one as a one-sided thing with the chance to grow into something a little more substantial, but I like the angle of Natsu having a crush on Leixia because Leixia's the first girl her age Natsu's been able to have any sort of meaningful relationship with; combine that with Leixia being cuter than a girl her age has any right to be and the bi vibe I got from Nats, and you have the start of a nice yuri angle more innocent than most of the popular girl/girl pairings (albeit by default, since most girl/girl involves Tira, Ivy, or both.).
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: Considering Siegfried on the "taken" pile and not really thinking pairing her with Raphael works, the only guy I could really see Ivy ending up with is Maxi. For starters, he's one of the few that won't grow old while she stays 32 until the end of the world, or at least one that won't outage her right away. He's a snarky pirate badass, she's a damaged but tough as nails lady, I could see some interesting chemistry there. Ivy needs someone she can trust in and consider an equal more than she needs a gimp, I think.
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: Note that I said the only GUY is Maxi, 'cause I privately think it's a lot more likely Ivy's into girls. The timeskip and Ivy's timelessness gives Talim some time to play catchup and serve as something bright and pure in Ivy's life, and I think that Ivy's experience contrasted with Talim's kindness and optimism could allow the two to help each other grow and be happy together. If Talim's unavailable, I also kind of like the idea of Ivy having a relationship with Shura and Valeria from IV and III, respectively. Shura's bi, extremely open about it, and always looking for conflict; paired with Ivy, it could make for an interesting if mostly physical relationship neither's able to maintain for long because they're both too dominant for each other but neither can walk away from because of the challenge it provides. With Valeria, I could see Ivy having a more understated, mature relationship where both parties understand and love each other, but it'd probably work out badly since Valeria is mortal, Ivy's reluctant to let herself be attached to anyone, and in all likelihood Ivy's dad is the reason Valeria's is dead. Although that could result in them teaming up to take Cervantes down and sailing of into the sunset instead, I dunno.
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: Because we all know Le Bello is swimming in bitches. :P
and 
x Vercci, but I think those are canon already. Therefore:
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These two were made for each other
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Just going out on a limb but these two would've also made a cute couple because they got so much in common (i.e. both being in April, people find them annoying, etc. )
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Because you knew Mina was going to make Yun into a man
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Goth kids in love...'Nuff said
