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xDD I love this topic.
My favorite shonen/shojo ai pairings throughout the FE series would have to include...

FE6:
Alan/Lance - I always pair the red and green cavaliers. I don't know why. Something about being Christmas colors together gets to me.
Percival/Elphin - I won't put why because of possible spoilers but it's at least a huge man-crush on Percival's part. xD

FE7:
Lyn/Florina - Florina is "shy around men" and Lyn's her best friend. Though I will admit that Hector/Florina is damn adorable but that's a different topic.
Kent/Sain - Red/Green Cavaliers again. xD
Raven/Lucius - ... Do I REALLY need to justify this? xD
Lloyd/Legault - I don't know, these two have background. A lot of it, it seems, from their boss conversation/morph battle. Legault calls Llyod's morph "a handsome one"? I don't know leavemealone ._.;;

FE8:
Kyle/Forde - Christmas cavaliers. xD
... I don't know, there aren't that many slash couples I like in FE8 because there's so much potential for a ton of straight couples. =/

FE9/10:
Ike/Soren - I don't care if this one's romantic or platonic. I just like their relationship dynamics and how Soren is SO OBSESSIVELY LOYAL towards Ike gets me. :<
Elincia/Lucia - Lucia is so protective over Elincia, and she's her milk-sister and and it's cute. :<
Kieran/Oscar - BECAUSE.
Calill/Nephenee - Yes, I KNOW Calill has a canon relationship with Largo. But Calill/Nephenee is adorable and funny and the idea makes me laugh. xD;
Tibarn and/or Naesala/Reyson - ... "Protector of the Herons" vs. "Old friend" ... Reyson totally doesn't seem the type to be straight anyhow >>;

That's all I can bring to mind right now >>; I'm sure I have more, though xD

I don't like Naesala/Reyson.... D: It's becoming way too popular and I see them as platonic.

Raven/Lucius will always be the #1 guy/guy pairing for me in FE though, because.... goodness! Even in the US 'censoring' they have an ending together. XD

I also mostly consider Ike/Soren to be platonic as well, but I can see why they might be a couple. Still...

Soren doesn't look like the type of person who could kiss, hug, or do other things couples do... neither does Ike, so it doesn't work in my mind.

On another note...

Wouldn't it be interesting if it were Lucius/Raven, meaning... Lucius topping? *bricked once, shot twice, tomatoed three times*

Ike is actually asexual by the looks of it for me.

Reyson I believe is the same way....

No other pairings come to mind, but Tibarn/Naesala hatesecks would just be too entertaining!! *shot, talon'd, beak'd*

Ahh, I freaking LOVE Leonardo/Edward. OH LEO. WHY ARE YOU SUCH A CRAP-ARCHER. ;-; If you weren't I'd actually use you and you could EARN that A support with Edward that I want so badly. ;-;

Edward and Nolan support is freaking amazing, though. Freaking. Amazing. Too bad they make an odd wtfpairing. >_>;

Also, Wrath, imma have to disagree with you on Boyd/Ike. There's no way Ike would bottom. >_>;

Ooh, I'm not the only one! Their A support is awesome. I was kinda disapointed by how... short the supports are in the new game. neutral

Edward and Nolan? xD;

Hm, yeah, you're probably right. I just wanted to give poor Boyd a chance. Poor Boyd. Doomed to be uke forever. X3

AUuuuuuuugh don't EVEN GET ME STARTED on how crap the support conversations are in RD. They... they're RUINED. *cries*

And... Yes, Edward and Nolan. Especially since they're your best two characters in the Dawn Brigade (unless your Micaiah got superlucky with speed, I guess... PFFT) and since Nolan is Earth affinity that means that they get tons OF EVADE from thier supports and it... it makes me happy. As a romantic pairing it's totally Leonardo/Edward but so far as support bonuses go Nolan and Edward are AWSUM.

Boyd seems like a seme person. Just not to Ike. Honestly, the only person I could ever, EVER see seme-ing Radiant Dawn Ike is the Black Knight. But only after a lot of beatings. And pain. And ********. And only with a lot of... uh... "swordplay."

Path of Radiance, Adorable Ike, however... I could see a few people semeing him. Mainly BK, Volke, Shinon, Haar... Er... Even though I don't even SUPPORT any of these pairings.

I dunno, though. Volke/Ike sounds like a LOLWTFAWSUM pairing to me for no apparent reason. xD

It's because Volke is flexible. xd

And they're both awesome, so yeah.

I think that's why I like VolkexBastian.

@Sue - Kieran/Oscar onesided is freaking hilarious. Especially when it's onesided both ways... Like, when they like each other but neither thinks the other could never possibly like him. There was a fanfiction I read like that once... but I can't remember what it was called.

gonk Yeah, Boyd kinda sucks like that. He's just not pairable.