An appendix document accompanying What Shadow Generations does for (or to) Shadow's character.
The following are a list of observations made of writing decisions in Shadow Generations that undercut or countervail previous material—be that in different games, Dark Beginnings, or even Shadow Generations itself.
Not all observations listed are of equal weight; ones with caveats to them are accompanied with an additional note.
Dark Beginnings and Shadow the Hedgehog confirm that she is aware of this fact he has Black Arms DNA, but Shadow Generations never establishes from what point in time these versions of the characters are, we don't know if Maria has learned this by that point.
NB: It is arguable that she wasn't aware of him being made to be a perfect soldier despite being aware that he was constituted partly out of Black Arms DNA
When Shadow says this to her before he goes off to confront Devil Doom, he smiles at her and she smiles back, implying they have had a conversation about it beforehand or that she at least knows what he's referring to.
Maria's dying wish to Shadow was for everyone on the planet to have a chance at happiness. But the key word is 'dying'. Even if we do not know exactly what point in time the Maria that appears in White Space is from, we can say with certainty it is before she died. There is also no indication in the story that Maria ever disclosed her sentiments to Shadow outside of her dying moments.
Why would Maria know what Shadow is talking about when it is a wish she had not yet disclosed to him?
The discontinuity is more prominent due to the fact that in Maria's first interactions with Shadow in White Space, she asks questions of him showing that she's confused with information she hasn't encountered yet, e.g. her question as to how Shadow grew so proficient with fighting.
Maria is now born on Earth, which was purposely left vague in past games. Establishing this as a new plot point arguably diminishes the weight of Maria's previously established wish to see the planet below.
NB: Only place where it's "confirmed" is just the SA2 Strategy Guide by Prima, which might not be a reliable source
NB: In side missions in the overall game, NPCs like Rouge feature in the levels as you complete specific missions in mind. Though this doesn't constitute as a narrative explanation for NPCs' capacities to appear in specific zones or environments, it technically means that we see NPCs be able to appear in such zones without issue.
In the final boss battle, Devil Doom induces Chaos Control despite not having access to a Chaos Emerald.
NB: He does have the ability to teleport in ShTH but this ability is not accompanied by a Chaos Emerald or the invocation of the phrase 'Chaos Control'
Shadow does not do anything for the rest of the story after thinking this to achieve his goal. Only in the last few moments in the final cutscene when Shadow shows panic at Gerald and Maria fading does he consider retrieving the Chaos Emerald he gave to Rouge, suggesting he forgot the thought to himself about diverting Maria and Gerald's fates until it occurred to him that he could use the Chaos Emerald to somehow save them.