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Sonic the Hedgehog
In Sonic Unleashed, towards the start of the game, when Sonic turns into a werehog for the second time and muses to himself, "I just need to be careful who sees me like this." Turns out that nobody in the game cares that Sonic has assumed this new monstrous form - not even Tails or Amy Rose, officially neutering the werehog as a plot device for the rest of the game.
At the start of TLE, Mephiles shows up and shoots Sonic In the Back, in order to make Elise cry. He is a time traveller. He could've done that at any point since Elise met Sonic and bonded with him. One theory is that he simply prefers manipulating people to try and do it for him, and/or is a coward.
Elise apparently never cried, not even once, from ages 6 to 16. Not even when she learned her father was dead. Also, killing her also releases Iblis. She could've gotten a car bomb or sniper rifle, since he had literally all the time in her life to try and kill her.
Speaking of making people cry, Robotnik's plan was to gain the Flames of Disaster from Elise. Yet at the end, he's disgusted by the fact that Mephiles had to make her cry to do so, which was really the only way. In short, Robotnik invaded a kingdom and nearly caused a princess to commit suicide over a plot that he himself believes is morally unjust. Does evil have standards here or not?!
In Silver's ending, Blaze seals up Iblis inside her and has Silver transport her into another dimension. This explains both her pyrokinetic powers and how she could be both from the future and another dimension. However, this is completely ignored in future appearances, meaning Sega drew up one of the most plausible plot points in the mess of Sonic 2006, then retconned it for no reason whatsoever.