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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 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.
After released from the status tube by Rouge in Eggman's base, Shadow suffers from amnesia after his fall from space in Sonic Adventure 2 and he has to team up with Rouge and Omega to find Eggman for their respective reasons. Later on, Team Dark discovers not only the fake Eggman but also the destroyed Shadow android, which caused Shadow to believe that he himself must be one too. Then Omega assures her that the real Shadow must exist somewhere. One thing: Isn't the real Shadow with you guys for the whole entire time? Of course, in Shadow the Hedgehog, Eggman revealed to Shadow during the final boss that one of his robots saved him from the fall, and that he was never an android after all. Well, thanks for wasting all of our good time for the black hedgehog's character arc, SEGA.
It also should have been extremely easy to check if Shadow was an android. X-ray anyone?
Team Rose's story was a bit senseless. The only motive the team has to do is find Sonic, although that's mainly on Amy's part. In the Team Sonic vs Team Rose scene, Amy acts like a Stalker with a Crush towards him and threatens to fight him if he refuses to marry him, not to mention that Team Rose accuses Sonic for stealing Froggy and Chocola during the fight.
There is the cutscene where Team Dark appears in front of Team Sonic. Although Tails and Knuckles were in shock to see Shadow alive, all that Sonic has to say is "Talk about stubborn and full of surprises!". Uh, Sonic? Is that a proper way to treat someone who you thought was dead after a tremendous fall into earth? This cutscene was one of the reasons why Shadow's return was a lackluster.
Shadow the Hedgehog is filled with a lot of wall bangers, being another notoriously mediocre Sonic game.
In many stages, whenever you attack one of the allies, whether it be a GUN soldier/robot, Eggman's robots, or a Black Alien, you will earn yourself a rebuke from your partner accompanied by them. Have they ever realize that same guys that you attacked were the same ones who tried to kill you in the first place?
The GUN Commander's blames Shadow for the deaths of everyone aboard the ARK, including Maria, whom he was close to the same way Shadow was. Let's get this straight. How can you blame someone for the deaths of everyone even when they were in progress of being created? Better yet, how could you work for a military organization who killed your best friend in the first place? It seems as if that guy hasn't really take any medication for his head when he was a child.