Judging how the plot take turns my speculations are
- The relation between Mio Takamiya and Itsuka Shido.
- Phantom reason calling Shido, Shin including their past.
- Phantom relation with Mio Takamiya (First spirit) as herself (Reine) said havent got a good sleep for 30 years.
- Phantom (Reine) plotting to complete the Spirits Tree. Also the reason She called them Child and his reaction to Shido calling her looks like a "Mother".
I recall that Westcott once called Shido, "Takamiya", linking him with Mio Takamiya (and Mana Takamiya) would later explain his relationship with her. Now all that matters is his previous Real Name. Was it Shin Takamiya? Theres defenition behind Shin name which is "Origin/True".
The Reason Woodman fell in love with the first spirit and make another countermeasure to protect them.
Westcott main reason of summoning the spirits might be order to get stronge or conquer the worlds perhaps?
Ellen backgrounds, According to information she is 30+ which doesnt make any sense? Woodman looks somehow older than others two. Did they somehow summoned spirits during their childhood? If Woodman age is around 14-20 during the first spacequake it would make sense he looks older but it seems the age doesnt apply to other two (Westcott and Ellen) unless they're a spirit or took somekind of drugs to slow their aging.(Also her sister as Woodman secretary, while her as Westcott secretary)
Main Antagonist wanted to become immortal or stronger for whatever reason he has by controlling/having/taking spirits power.
Reine desire to combine all Spirits power to create something? or maybe return to their world.
Reine, Mio, Woodman might had a promise or reason behind the Creation Ratatoskr. ("The organization called Ratatoskr was an organization created for Shido's sake."
Shido/Shin as the person who hold the key and as a vessel for the ending of the series.
Not so complex but the Missing memories making it harder to link all the pieces.
Sorry for the late reply, since it took me some time to fully understand the context of your speculation.
Shin could means many things, depending on the kanji used, but "origin" is not one of them as far as I know.
As for Westcott, his mind seems to be waaay too warped for something like "conquer the world", considering that he hold "peace" with contempt. Immortality and absolute power sounds more plausible, considering he's so power-hungry to resort to inverting the Spirits.
Ellen might've been treated with Spirit's mana or something like that to increase her battle prowess. As for Reine's motivation, we don't even know much about her to even begin to speculate about her wish right now, but Woodman had stated that having Shidou to seal the Spirits is a rather precarious strategy, but the Ratatoskr had to go through this plan because Kotori had sealed her powers inside him.
And it's not just Shidou's origin that needs to be unraveled either. Tohka and a handful of Spirits (Yoshino, Yamai sisters and Natsumi) also have an undisclosed, if not a mysterious past.