Like my other post, the game is simple...
You name a plot point, issue, theme, character, arc, anything that annoyed you in the comics and then get to replace it with your own idea. Remember complaining is never productive, but constructive criticism in the name of building a bigger and better story-arc and learning from other's mistakes doesn't just improve the tale being told, but also improves you as a writer (which is a very practical skill to develop I might add). Responses to other peoples' ideas should be added after your own ideas are said, as to not confuse things.
Allow me to go first...
Multiple Alternative Universes.
I hate the idea for multiple reasons (*rimshot*). The biggest being something people don't usually think of. If we subscribe to multiverse theory in our writing, say there is a vast and infinite array of Sonics battling out there in the multiverse, we cheapen Sonic's story and actions into insignificance. So what if Sonic Prime saves Tails in this issue...somewhere in the multiverse a new reality has just been produced to where he didn't. Every choice that is made is canceled out, and the hero's endeavor to improve things around him is useless, for every good deed he does there's a million-million worlds where the deed was never done or malignant in the first place. The characters aren't special and their choices don't matter in the grand scheme of things.
Now this is not to that other universes can't work if we say they are different and unique and have their own problems (as long as there are no carbon copies waltzing about). In a different world with different rules and problems interacting with Mobius can be interesting, much more interesting than the giant potential existential crisis that is the current multiverse. To further illustrate the darkness of my point, go read Silcon Lemming’s the Quantum Man: http://www.youtube.c...h?v=MvSVHEQx1wQ (just apply it Sonic and its instant nightmare fuel for us FUSers). Might I also reference that the writers at DC have all but abandoned this mode of thinking, and nuked their multi-verse a long time ago for this reason? There are divergent universes, but there is somehow a limited amount (around 52).
So, how could we do multi-verse better?
I have already suggested two solutions. But I want to stick with one: we make different and finite amounts of unique worlds which have no simulacrums. Compared to the self-defeating and lazy writing of the former (I mean how easy is to whip up a cheap anti-sonic villain to be the dramatic foil of the day and all that jazz this way?), this would force the writer to craft a deeper and engaging lore to the Sonic Franchise, and add more potential for dynamic and meaningful conflict.
Remember Satam my fellow FUSers! Sonic's actions always meant something and it wasn't a confusing mess and victories meant something! Let’s keep the story contained or make the alternate worlds so unique as to keep everything clear-cut and meaningful.