Plot Hole #1 - Ever since Sonic Adventure 2, it's been proven that one can use a single Chaos Emerald to warp simply by saying Chaos Control. There is no way that Shadow found this out on his own, which means that he must have learned it from somewhere. Considering that it was taught, you'd think that Dr. Robotnik would have figured out how to do this by then, therefore giving him MUCH more power than he gives himself. Plot Hole #2 - Regardless of whether the story of Sonic '06 was reversed or not, the Chaos Emeralds still have the power to create a time-space rift to travel through time. Shadow originally knew how to do this before Shadow and Silver accidentally created the rift, so that means that Shadow even knew about time travel this way. However, how did he find out? He must have learned it from somewhere, unless Shadow got REALLY lucky. Again, Dr. Robotnik would've eventually discovered this and used it to his advantage. Heck, he could already time travel in Sonic CD, which adds ANOTHER plot hole. Plot Hole #3 - Where was the seventh Chaos Emerald in the first game? Based off of ancient legends and manuscripts within the Sonic universe, the seventh Chaos Emerald is present. Does this mean that Dr. Robotnik technically had one of them on him? If so, he could USE CHAOS CONTROL! If not, then where was it? Was it lost? If so, how did it suddenly re-appear? Plot Hole #4 - How is Dr. Robotnik able to build a bunch of ships and machinery within a super short period of time? Think of the Egg Fleet from Sonic Heroes, the time machine in Sonic '06, every boss he's ever created, three copies of the Egg Carrier, all of Eggmanland, and so on? There's NO way just one person has been able to build that at once. He HAS to have a group or something to help him do it. Yes, I'm aware it's fiction at this point, but it's still unexplained.