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".
Last thing was about the First Spirits Appearance " She was summoned into the world by Sir Isaac Ray Pelham Westcott, Ellen Mira Mathers and Elliot Baldwin Woodman through unknown means."
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 grammars)