I've been studying 06 story very carefully and after long considerations I think I have the theory that covers all the plot holes; it explains how time travel works, why no one used it more often, why only main characters remained in "End of the World" and even how Elise could hold that blue emerald for all these years
1 What about Ian's explanation?I don't know if Sega gave it to him or did he created that explanation on him own, however his 'four timelines' theory doesn't make any sense. Why would Mephiles send Silver to the past? Iblis is already free. Besides, if Silver going back in time changes 1 timeline into timeline 2, and Sonic with Elise changed 3 into 4, who caused change between 2 and 3? There is no time traveler who would change events.
2 Ok, how time travel works?There are two basic theories how time travel works, I call them "crossroads" and "detour".
"Crossroads" is the idea you seen in "Back to the Future", "Zelda: Ocarina of Time" or "Sonic CD". The future can be changed. Your want a cookie, but your brother already ate it? You go back in time and eat it first. That created two timelines, 'hungry you' and 'hungry brother'. Whenever first timeline still exists or gets erased depends o the fiction.
"Detour" is theory from "Harry Potter", "Gargoyles" or "Rise of Lyric". Future is set in stone. If you go back for that cookie then either your action will actually cause your brother to eat that cookie or (rarely) make no effect.
And yes, I know that it doesn't make sense. There should be 'timeline prime' in which there was no time travel and you ate a cookie, but there isn't. "Detour" suggest that time travel already happened before you decided to go back in time, so your action A causes you to take action B, which will cause action A. Cause and result change places. Still, many famous stories use it, so who am I to judge?
With that knowledge you can see that time travel in 06 fits perfectly into 'detour' category. Egg Carrier crashes (action A), which causes Sonic to go back in time to save Elise (B), which causes Egg Carrier to crash. Or Shadow seals Mephiles, which allows him to release him later, which causes him to go back and seal him in a first place. There is more examples, but you get a drill.
3 But why heroes don't even try to change past?That depends from each hedgehog.
Sonic doesn't have a good reason to risk messing with time. He does it only as a last resort, like when Elise died or when he was stuck in future.
Silver has no choice, time travel is the only way to save his future. However after his team-up with Shadow two things happen.
1 He has no ideas how to stop Iblis in the past ('kill Sonic' isn't an option anymore)
2 He learns how to stop him in a future; by sealing him in a person.
Lastly Shadow could easily call Sonic, use Chaos Control and stop himself from releasing Mephiles. Who knows, maybe he even considered it. But from all main heroes he's most aware how time travel works; first he saw Omega in the past (event A) which caused Rouge to send him there (event B), and then learned how Mephiles was sealed. With those two examples of 'detour' he might've guessed how it works and that this plan wouldn't work anyway.
4 Fine, explain Mephiles actions.This one is mostly a guess, based more on loose evidence. I think that Mephiles
1 knows how time travel works (so he knows that future is unchangeable and everything is destined to happen)
2 HOWEVER, he's also destined to do them. That's why he can't just go into the future and fuse with Iblis: he must release him from Elise first.
3 he also PARTIALLY knows the future (either by some extra power we don't know about or by simply looking into the future newspapers), but not all of it; he knew that Sonic's death will free Iblis, but he thought that Silver will do this.
That's why he tries to convince Shadow into joining him: he plays 'self fulfilling prophecy'. Shadow would become evil and humanity would turn against him.
He also probably knew that Silver will show up in a past, so he decided to cause to help him do it and manipulate Silver into killing Sonic. Then Silver would cause his own future (instead his actions had no effect).
5 You're theory has one giant hole: future WAS changed! Sonic erased Solaris from existence, remember?Yes, but when that happens? After Solarist started to 'destroy time itself'. My guess is that with world damaged on psychical level, rules of psychics (and time) can be damaged to and work differently.
6 You mentioned that you know why only main cast appear in this void?At first I was going to just say 'plot convenience' and ignore it, but then I noticed: Elise is special because Iblis was sealed in her. Everyone else has one common trait: they are time travelers. Team Sonic and Dark did this to escape from the future, SIlver at the beginning of his story.
And Amy and Eggman? They passed this test waaaay back in Sonic CD. Sure, we never seen them doing that, but someone had to install those machines in the past and I doubt Metal has enough skills to do so.
But then again, 'plot convenience' sound good too.
7 So what's with Elise's emerald?This is a fun one: we know that Sonic and Elise went back in time and erased this game from existence. But how much did they changed? We don't know how far they went, it could be 10 years, it could been hundreds. Butterfly effect could change a lot.
So I believe that there are two major timelines.
Timeline 1 (Sonic 1991) in which all games happened, except for Sonic 2006.
Timeline 2 (Sonic 2006) in which 06 definitely happened (and probably Sonic CD), but other might not.
Maybe other echidnas still exist, which would explain why Knuckles isn't guarding Master Emerald.
Maybe Maria was never killed, which would explain why Shadow works for G.U.N.
Definitely one Chaos Emerald was in Elise hands all this time, so Sonic never went Super before. That also explains why Shadow didn't tried to go Super solo to fight Solaris; he also never did that before.
So yes, 2006 timeline was first, but after Solaris was destroyed it was erased in favor of 1991timeline.
8 I still feel like you missed something.Sigh, yes there is one plot hole that I haven't explained: Silver's future. How can exist future destroyed by Iblis, if Mephiles already fused with him into Solaris and they destroyed everything completely? I have two theories, but they aren't very convincing.
1 Mephiles didn't fused immediately with Iblis, he waited years for Silver (because he believed that Silver is necessary for his plan). It didn't looked like this, but remember that Mephiles starts destroying time. It could mess with time perception and bring time travelers from different moments in history.
But even if you buy that nonsense, there is easy counter argument: where is Blaze? If she sealed Iblis in her, then Mephiles can't fuse with him. If Mephiles screwed logic he was using so far and changed the future (by removing this event) then Blaze should still live and be with other time travelers.
2 This scenario suggest that timeline 2 (2006) didn't disappeared after Sonic and Elise went back in time.
Instead story went further; Solaris was defeated, but not killed (if Iblis can't be killed, how Solaris would). So the only thing to do was to split Solaris once more and seal Mephiles and Solaris in new prisons. It worked with Mephiles (make better scepter, bury it very deep. Easy), but not with Iblis (because sooner or later his princess prison will die of old age) and he finally burned the world, creating Silver's future.
You can argue that this can't be true; this timeline was erased when Elise blew up the flame. Well, maybe it did. However it kept going for a while, for future events with Silver to happen, since they are required for this story to happen.
Uff, I'm done. So what do you think? Good? bad? TL;DR? Yeah, I bet it's going to be the last one.