After reading Sonic #225 I've been going through my head thinking about the shock ending(after recovering from the shock). I came across some of the same points that are in both Sonic #225 and Spiderman: One More Day.
1) The ball and chain: Sonic and Sally have finally got back together after nearly 100 issues of being broken up. Unlike Spiderman and Mary Jane, Sonic and Sally work amazingly as a team so there is no reason for them to be broken up again.
2) Pain of love: In issue 225 Sally is killed by Eggman with a machine gun. A far better way to get rid of a love interest than having the lovers walk past each other pretending nothing has happened in their past. Sally getting shot makes a lot more sense than Aunt May who should have died awhile ago.
3) Real evil: Unlike the devil in Marvel comics, Eggman is an evil and scary villain that has in many occasions won battles agents the heroes of the world. Even when Eggman isn't on the page he is talked about of what he may do next.
4) Reset: The new world in Sonic is going to be Sonic having adventures from the games Sonic 1&2 for a little while then things are going to be more or less normal after that. The readers knew the change was coming, how long it may last, and that things will return to normal with some differences.
5) Magic ≠ Science: In Marvel for the devil to change the timeline he had to just wink and smile, where as in Sonic Eggman had to take his time to prepare. After having his city destroyed Eggman lost nearly everything, so he had to pour his remaining resources in to his last standing base with lots of hidden halls and rooms. While making his ultimate weapon he lost his mind for a while, when he became sane again Eggman have a new outlook on his grand plan. After many issues of construction, finally getting a rare limitless power, and using an army of slaves to send supplies to him the ultimate weapon Death Egg launches to the horror of everyone that it was built in front of them the whole time. With time, planing, and effort is how an evil genius makes things go the way he wants.
6) Can't touch this: Before Eggman pushes the big red button of doom a nemesis of his who also has a rare limitless power to use magic to stop Eggman, but has no effect thank to magic proof hull. Unlike Marvel where some hocuss pocus can change anything, in Sonic's world magic has its limits. So the line "a wizard did it" can't be use for plot holes that are lying around.
7) Cloning clone saga: Sonic also had his own clone trouble that was handled better. In Sonic X #25 Sonic had to deal with a hand full of clones for just the one issue. Unlike Spiderman, Sonic's clones were just like him but a different color each(not counting the last one)so they weren't as crazy as Spiderman's clones. Sonic's clones were made by a group with the smarts, resources, locations, and time to do it. The best part about Sonic's clone saga is that it only lasted the one issue where as Spidermans took years and still doesn't make sense.