Here's something I realized during one of my hearings of Sonic's first Image Song, It Doesn't Matter. It is obviously a song the describes Sonic The Hedgehog the character, but if you delve into it a bit, it can also describe what's going on with Sonic The Hedgehog the franchise. Let's take into consideration the main chorus line:
"It doesn't matter now what happens/I will never give up the fight!" seems to mean that Sonic isn't going going to stop moving on.
"Long as the voice inside me says "Go," I will always keep on running" and "There is no way to stop me from going to the very top!" are similar to the first. Sonic isn't going to quit until he stops Eggman once and for all, and unless Sonic Team makes a game where that happens, the franchise isn't going to stop, either.
"It doesn't matter who is wrong or who is right!" may be a credo Sonic has, but it can also extend to everyone involved with the franchise, from the people developing the games, to the people who are (or should be) enjoying them. Sega and Sonic Team may add some strange features, but who cares? It's just a game, and games are a form of entertainment. You shouldn't let simple entertainment take over your life. This is what Sonic's song is trying to convey. Don't let the little things get the better of you and keep on moving. Hopefully people will be able to take this to heart after Generations comes out...
I just realized that Chaos has a blue body and green eyes— just like Sonic does. And those things on Chaos 0's head look like Sonic's quills.
In E-102's story in Sonic Adventure, his perspective on good and evil becomes challenged when his brother, E-103, stares at him pleadingly, an image that seems to haunt him. In short, it caused a change of heart. E-103's designation is Delta (Δ),which means "change in" when applied to mathematics.
In Sonic 3 & Knuckles, the Master Emerald was in the Hidden Palace zone. But in Sonic Adventure, it's in its shrine on the outside. How did this happen? Why did this happen? A theory comes to mind. After Robotnik told Knuckles that Sonic sought the Emeralds for immoral purposes, Knuckles hid the Master Emerald just as he did with the 7 Chaos. After Robotnik was beaten by Super Sonic, it's possible Knuckles just returned the Master Emerald to its original shrine; the last we saw of it in Sonic's ending was that it felt out in the open of Angel Island, and we never saw Knuckles take it back to the Hidden Palace, and perhaps he couldn't, considering we don't know how much damage Robotnik caused it when he broke in.
Something it took me a while to notice about The Rashomon style of the storylines: everyone's personality is subtly shaded to be more like the viewpoint character's (ie. everyone has more of an attitude in Sonic's story, Sonic is more polite in Tails' story, ect.).
Not to mention, the outcome of the battles between playable characters changes depending on who you're playing as, furthering this point.
When playing in Adventure Mode after beating the game, it's always daytime except as Gamma, when it is always night (at least, in the Dreamcast version). Why is it different for Gamma? Because he dies the following day.
In Unknown from M.E. (Knuckle's Theme) one of the lines is "unlike sonic I don't chuckle" but in his first game Knuckles is seen laughing every time he appears while Sonic never does.
Perfect Chaos path of destruction suddenly starts to seem extremely bad if you consider how many innocent people must have died. He creates a tidal wave that completely floods the entire city, causes water to rip through and destroy buildings, and basically causes a path of havoc similar to that of a extremely disastrous tsunami. I mean, JUST LOOK at how destroyed the city is in a matter of only minutes...at the very least, the people in the building would all die or be SERIOUSLY injured. Again JUST LOOK at the cut-scene where the water rips through the buildings. ...Don't forget this was a game primarily aimed at kids. Not to mention that after a certain and rather recent real life tragedy...this has become a major source of Fridge Horror.
In Knuckles story he sees Gamma in the nearby the Master Emerald alter, but Gamma doesn't visit this area until later in the game. Seems like a continuity error until you realize that as Gamma makes a beeline for Eggmans jungle base it means he's collected Froggy at this point, and is currently in a flashback. Tikal gave Gamma a vision while taking control of his body to lead Knuckles back to the Egg Carrier.
Add to that, Tikal giving Gamma a vision seems a random and superfluous act compared to the actual heroes, until you realize that in his own story, Gamma was Eggman's most pivotal minion in helping power Chaos and was seconds from destroying Sonic (who was destined to stop Chaos and save humanity) had he not gained a conscience. Tikal's conversation with Gamma mostly consists of subliminal claims of good will ("I see you are not one of them." "My hope is that one day we will all understand one another.") as if to try and bring empathy from the droid so he won't be able to fulfill his duties to Eggman.