Okay, so World Embryo is a relatively fresh canon. There are 31 chapters out! A lot has happened in them already so far, but this is Moriyama we're talking about so there's also a lot of mysteries and unexplained things that will be revealed. Here is a list of the things I wanna know.
What Youhei did for Rena
This one's actually a bit dicey because it only comes up in the Chuang Yi (Singaporean) translations of WE, so it... may not be true! Anyway, in those translations, Rena mentions Youhei having done something for her in "her darkest hour". In the scans, she talks about radiance and preparing her soul. If I assume the Chuang Yi translations are right in what they imply, then Youhei helped Rena when she was at her worst, at some time in the past. If not, well, I'm sure there'll be more flashbacks to him anyway.
Youhei's time with Hayato as a partner
TWO YEARS PREVIOUS, Youhei and Hayato were partners, not Youhei and Rena. What's more, Hayato wasn't wheelchair-bound yet and he clearly is a jinki user as well. I'm guessing there must have been a horrific accident or something that took Hayato out of active duty and required Youhei getting Rena as a partner instead.
Full effects of 'Lost Rebound'
I'm not sure if they're really going to go into more depth on Lost Rebound other than what they've already said, but it'd be interesting if more victims of it appeared. Obviously Shizuru wasn't all that affected when Youhei was forgotten, but that other girl was. Rena said that it can take years to repair the damage left by the memory holes a Kanshu-infected human leaves. Also, photos are unaffected; there are still plenty of pictures of Youhei in Rena's room and Hayato's house. Not so sure about things like phone bills and personal records.
WTF Takao is up to
Yeah, well, all we know is that he talks on the phone to someone and he's a jinki hunter who gets super pissed at the idea of giving jinki to people. I bet it's a while before we learn anything about him.
Rena's backstory
...has all the hallmarks of Chrno's backstory, in how it's being handled. So I expect there'll be a lot of ALLUSIONS to it before there's suddenly a bunch of chapters solely dedicated to it. Rena mentions having lost an important person who can never be forgotten; obviously this could be and most likely IS Youhei, but given that dream of the train, I wouldn't be surprised if the guy standing behind her is important too. He had what looked like her trenchcoat on. And she doesn't really remember her past, so it might be Kanshu related. I also expect Youhei to figure in it later, since they've known each other for two years. I'd also like to know why, out of their "group" (Youhei, Hayato, Suzu, Joe, Clara, and Rena) she was the only one who seemed not to have a partner. They made it pretty clear that all jinki users are in teams of at least two, so that if one becomes infected the other can kill them. SO WHERE WAS HERS? OR DID SHE JUST NOT HAVE ONE?
Where the hell is Riku's dad?
He just up and left after Amane's disappearance/death, and there hasn't been much sign of him since. Shizuru mentioned thinking of contacting him, but there's been no obvious sign of him. I mean, he could just be at work (because parents are disposable in manga) but it's a bit strange that he left so soon after that. Riku doesn't mention him at all.
For that matter, is that hospital director the cause of everything?
I'd be pretty surprised if he doesn't come up again. Amane was SEEING HIM for some reason, he was IN THE HOSPITAL when it exploded, so I'm willing to bet that he had something to do with... whatever went on in there. Possibly he's even the 'source of the infection' and the one who turned Amane into a Kyuuki/Coffin Princess/whatever the hell she is.
NEENE
Gets her own heading because lolol. She is obviously bad news! Very cute bad news, but still. The latest chapter reveals that she feeds on memories in order to grow. This, coupled with her disturbing habit of making people comply with whatever she wants, and the 'source's' declaration that she's actually the queen of the Kanshu, paints a pretty foreboding picture of what's going to happen when she finally hits Amane's age. But, the real question is...
Will Riku ever stop being a complete dick and realise that Neene becoming Amane is not necessarily going to be A Good Thing where he can finally say "I LOVE YOU!!1" and put it in?
Not for a while, I bet. But he BETTER get a cluebat to the head before canon's over, because I trust Moriyama not to have had Youhei die to save him just so Riku can be accessory to the world's destruction. Even if he is thick as two short planks. Love him, but lord. "But, if Youhei ever found out I was deceiving his own allies... would he blame me?" EARTH TO RIKU, YOU MIGHT BE ONTO SOMETHING THERE.