I'm an obsessed Itsuki freak, so my first question is, do you think he's alive and in the new universe? He was one of the few people Ayato trusted, and they were twins regardless of being genetically engineered, so if Ayato is alive, would it be plausible to assume that he would still have created him in his universe?

We can safely assume he's indeed alive and well in this new world that Ayato created. Though we don't know the exact details of it, only assumptions. If you remember from the last episode, Quon was referring that she would like to be part of Ayato's life in the next world, and so she was reborn as his daughter. Itsuki said he wanted to be with Quon always, so I can assume two things: He would meet Quon later on and date her, or be born as a brother. Like I said, these are only 'educated guesses'.

Also, Ayato has blue blood, so why was Itsuki's blood red, given that they are twins?

Both Ayato and Itsuki have red blood, but they have the Mu-Phase in it. Having the Mu-Phase does not make their blood turn blue, it's simply saying they're half Mulian and half Human. Quon and Maya on the other hand, are full blooded Mulians, so theirs is naturally blue.

At the end, when Itsuki said that he had found his blue bird, does that mean that he opened his eyes (the way he had told Ayato to do), and had realized that Sayoko was always pining after him? If so, then does that mean that he realized he loved her?

He realized Sayoko loved him when she stabbed him. Though I'm pretty sure he knew about Sayoko's feelings all along, as we saw that he wanted to please her (or toy with her) with the pendant he gave her that was part of a Dolem (of course he was just being a cold jerk and using her as an experiment). What he was referring in that he found his blue bird, is that he realized he loved Quon. Whether is romantic love, or family love is unknown (they're not related by the way).

What exactly did Quon mean by what she said when she saw Itsuki in the last episode?

Hmmm... I don't really remember the exact words that Quon said. But I'm pretty sure she meant that she also loved Itsuki, and would like to be with him in the new world as well. I'm pretty sure Quon has always hold some sort of respect and love for Itsuki, but Itsuki never really knew about it until she told him that. I believe this is also close to the moment when Itsuki told her how he felt by phone (the phone I guess is symbolic, since the scene took place in some sort of after life/different dimension... the same can be said about the TV).

(Thanks to Debby C. for the questions)

Maya was originally from the Mu world, she was transported to this world inexplicably along with Quon. As you know, Rikudoh was the one that raised her. During this time, Maya was just like any other girl, but sometime during her youth, Maya "awoke" as Mulian, and all her memories and skills as a Mulian came back, and she eventually became the leader of the Mu.

That sounds like the movie, I've only seen the movie once, so I don't remember much details. But I do know that Maya used to have a lover in the movie, and in the TV series she was always single. On both versions she took care of Ayato, in the movie Ayato was her real son, but in the TV series he was her adoptive son.

Bahbem simply wanted to play god, that's all. He wanted to create an artificial being capable of re-writing history to his own will. Of course the Mulians and the humans come into play, and want a piece of the pie too.

When the Mu first appeared in the sky, they simply wanted to co-exist with humans, but humans delivered the first attack, and so the Mu struck back with their Dolems. They never attacked first, though they were pretty offensive afterward and much more effective than the human attacks.

Yep, the movie is an alternate version of the same story. They wanted to tell the story, but with some changes. In other words, the movie and TV series are not related, each one tells its own version of the story. Kind of like comparing the Escaflowne TV with the movie.

(Thanks to indecentxposur for the questions)

That's partially correct. Before episode 19, Asahina (nor Ayato) had awaken as Mu yet, so they saw their blood red (as you saw in the train wreck in episode 1). After both Asahina and Ayato eventually woke as Mu, they could see the real color of their blood. And without the mind manipulation working right, it only sped the matter.

Also correct. However, at first he only thought of her as a friend. Asahina was still delusional that her blood was not red, so she thought that Ayato wouldn't accept her if it were. Which is what she's been meaning to tell him throughout the whole episode, along with claiming her love for him.

All Mulians have this ability, and from the looks of it, each Mulian has their own Dolem. In the FAQ I said (I believe so) that each Mulian in fact has two identities, their human self, and their Dolem self. One cannot exist without the other. Their Dolem form is kind of their defensive mechanism, though it is used more often than not as an offensive weapon.

If Ayato were a full blooded Mulian, he would most likely have a Dolem as well, but he's half Mulian and half human as you know.

Most likely because she was in so much shock when she found out she was not human, that her mind was not working right. She's new to all this Mulian thing, and just couldn't control her Dolem. The Dolem evidently started attacking out of control, and Ayato had to fight back.  The ghostly figure in Asahina's mind that eventually manifested towards her death, was her Mulian self.  That's the Mulian in control of Asahina's body, and also the one responsible for the Dolem.

(Thanks to Chris Thompson for the questions)

More to come upon request.