First, this does mention other pairings. I want people to understand where I am coming from. Please try to keep discussion intelligent in general.My biggest problem with the YoruHara ship is the way they act towards each other. Very business like. As someone who has been in a long distance relationship, their reunion in 51 is not romantic at all. Kisuke was trying too hard. He picked her up in her cat form and was making a big fuss over her return, and then he has milk ready. It's almost as if he was still trying to make it up to her for having dragged her into his mess with TBtP stuff. Meanwhile, she's like, "Cut the act, Kisuke. I know that you know that 'they' are here." Not a "How have you been?" or "Good to see you," or anything. And Jinta and Ururu had no idea who Yoruichi was. They didn't know her by name, either. Meaning Kisuke never discussed Yoruichi with them, and that Yoruichi was never around. This is also evidenced by Yoruichi's mention to Ichigo that she wasn't used to wearing clothes. That would imply that she was in cat form a lot.
I understand that Shinigami can live for thousands of years, but I just can't imagine staying away from the person I loved, the person I considered my soulmate, for that long and then being that cold when I finally got to see them again. In my relationship with Joy, it's hard enough to be separated for more than a few days.
Her reaction to Soi Fon on the other hand seemed more passionate in a way. More personal. At the very least, it was way more involved and there was more dialogue that we got to see. She teases Soi about yelling. "Heh. Calm yourself. I see your temperament hasn't improved." And then when Soi figures out it's her, she smiles and says, "Long time no see, Soi Fon." See here. And they banter. Soi's serious but it looks Yoruichi is having fun with it. Banter. Then Yoruichi teases her about being talkative. When she asks if her shoes were too big to fill, I get the impression that she may have been taking a dig at Soi because she herself was hurt that Soi didn't come looking for her or because Soi thought she was a traitor. She was lashing out to mask her own feelings, IMO.
Then there is this page, which we already mentioned is suggestive. I don't buy that Yoruichi would let Soi get behind her unless she wanted it to happen. Also, you might note where Soi's left hand is in the top panel. It's right on Yoruichi's waist. And you'll notice that Yoruichi moved ASAP when Soi brought out her shikai and Yoruichi realized that Soi was actually serious.
Yoruichi explains to Soi that she never showed her shunko because it was too dangerous, and she stops Soi when Soi tries to use it anyway. "It's still too early for you to use this technique." She cares about Soifon's safety. Which we see again on top of the Soukyoku Hill, here. It's very possible that Soifon was left out of the loop about Aizen because Yoruichi was trying to protect her.
Then in the flashbacks we see the many faces of Yoruichi:
happy face
dismayed face
food stealing face and "you cut your hair" face
Then back to the present, Yoruichi protects Soi again - this time against shunko: Here.
And another face, - - sad face? Regret face? It's hard to tell but it's definitely not "business face" IMO.
She just seems more natural and real around Soi compared to Kisuke. The only time she really put down Soi was here in TBtP when Soi was bugging about Kisuke, but Yoruichi herself was pretty business-like with Kisuke that arc. Here and then when she reprimanded Kisuke for worrying about Hiyori, here.
Yes, Yoruichi and Urahara work together very well. But so do Yoruichi and Soifon. They work so well together they finish each other's sentences! See here.
Finally, the Kon Radio stuff that people argue makes YoruHara canon...I disagree, it makes it seem more like Kisuke wishes there was YoruHara but Yoruichi doesn't feel the same.
Q: Have you seen Ms. Yoruichi naked?
Kisuke: Naked? Of course!
Kon: What?! That's inexcusable!!
Kisuke: Well, Yoruichi and I are very close. I really can't say any more.
Kon: Hmm...And?
Kisuke: I've seen parts of her beyond naked!!
Yoruichi: Hmm...
Kon and Kisuke: !!
Yoruichi: I see. I didn't know we were so intimate. Would you care to elaborate?
Kisuke: Aw, c'mon, Yoruichi. Not here...
Yoruichi: Don't be shy. "Beyond naked," huh? Let's start by checking out your bones.
Kon and Kisuke: N-N-NOOOOOOOOOO...
Here's a picture so you can see the facial expressions.
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And that's what I've got. Please feel free to add your own reasons, to argue with what I have up here, or just comment in general. 
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. They work very well together as a couple for some reason. They also bolth happen to be my two favorites in bleach. 