There's so much great nonsense in Sonic Adventure 2. The prison island cell being a Chekhov's Gun for act 3. Hedgehogs somehow being the only beings on Earth capable of chaos control and Super forms. Eggman being unable to decide whether he wants to take over the world or destroy it completely. Tails just... having the ability to produce replicas of the chaos emeralds. The president being introduced as a character and then immediately being dropped
But most importantly, the three possibilities for hedgehog lore:
1) All Sonic-universe hedgehogs are genetically engineered lifeforms made from the DNA of alien lifeforms
2) Completely coincidentally, hedgehogs are the ideal vessel for using the Chaos Emeralds' abilities, and Shadow is only the Ultimate Lifeform because of his immortality
3) Maria's will lives on in Amy, Sonic, or both, explaining their emotional connection to Shadow and callbacks to Maria
Like... was Sonic created by Gerald Robotnik as a successor to Shadow? Does Sonic also have Shadow's Black Hand dna, or is that the thing that separates them? What is Sonic/Amy's connection to Maria? What is GUN's goal as a paramilitary organization? Why was the ARK actually shut down? How did Gerald know of the existence of the Master Emerald? There are so many fun questions!!!
Wild theory time: Sonic was actually the one who knew Maria, but his memories were taken by Gerald after Maria's death and used as part of Shadow's creation. Maria... body? memories? medical data?? was used to create Amy just before Gerald died, as a form of reincarnation to atone for his failure to save her life.
Thus, Amy crushes on Sonic, Sonic and Amy both quote Maria to Shadow, and Shadow has faulty memories of Maria's dying wish, filling every single plot hole simultaneously