Probably some delayed effect as time settled. Since the ending picked up Sonic's party, Classic Eggman would've gone back to preserve the timeline. Regular Eggman was probably sent back into space before he found the Time Eater, or went back with his younger self and waited.
Why are the Wisps suddenly on Lost Hex? It's never explained how or why they're on the planet.
I always kinda took as they're throughout all of the universe, Lost Hex is just one of those planets.
There isn't an explanation, sadly.
Well, he did help the Wisps in Colors. This could be their way of repaying Sonic.
Finally explained in Sonic Runners by Tails that although most of the wisps returned to their home planet in Colors' ending, some wisps stayed behind on Earth.
If traveling to Lost Hex from Earth is as easy as just flying to it, why didn't Sonic, when the shit hit the fan, fly back to earth, gather up Knuckles and Amy and fly back? It's not like he can't fly a plane. It would have been the perfect way to bring Knuckles and Amy into the heart of the plot instead of having them sitting outside of it looking in. And even if Sonic wasn't in the mood for it, what's stopping Eggman from doing such? Or better yet, going to Team Dark for assistance? They may be at each others throats constantly, but Shadow is usually more or less cool with helping Eggman out if he has good reason, and THE DESTRUCTION OF EARTH is more than enough reason.
As far as Sonic and Eggman knew, the effects of the Extractor couldn't be reversed, so they probably thought they didn't have the time for any detours.
I thought Shadow was a good guy now.
He is a good guy now, he was just referring to being cool with Eggman if Eggman's being a legitamently cool guy.
Sonic thought he could be fast enough to stop the Deadly Six before the Earth died. Telling them to stay put and let him handle things was another act of recklessness.
Since when does Sonic bring Amy with him on his adventures? And he had enough problems as it was; she's usually a pain in the neck for him, chasing him all the time, trying to make him marry her, and getting caught by the bad guys.
How the heck did tails remove the (invasive looking) robotic parts? Even his eye was changed.
Probably that he also reprogrammed the machine to NOT surgically install the parts on him, but to make it look that way to fool the Deadly Six.
I thought he just grabbed some spare parts and stuck them to himself.
Related to the point about gathering up Amy and Knuckles up above, after hearing that everything on the planet was dying and having the life sucked out of it, what in Solaris' name possessed Sonic to tell Knuckles and Amy to stay put and think that was a GOOD IDEA!? You have a FRICKEN' PLANE, why not just make some trips and drop them off in Windy Hill, at the very least?
We already had a similar question, and the answer is that they didn't have time.
They couldn't even arrange an evacuation or anything? Amy brought up the problem to Sonic as early as Tropical Coast. At that point, Sonic and Tails were still bullshitting around without any real urgency. They had freed the Deadly Six, but that was about it and they didn't think that much of it anyway. It took until the third zone of Sky Road-at least two or three sectors away-for Amy and Knuckles to disappear completely. You're telling me that Tails-a fox who at any given time has two or three planes among other things-couldn't set up some sort of transportation for them? And it's not like he didn't have anything to do it with, both parties had a Miles Electric, which has been shown to be not just a video-phone but a full-on personal computer capable of nearly anything the plot needs it to do. It's also not like he didn't have the time seeing as Sonic does all the legwork, leaving Tails and Eggman behind to twiddle their thumbs in between cutscenes. They had PLENTY of time to save their friends. They just didn't.
Well, Sonic saved the world, so I don't see why this needs to be an issue anymore.
I've seen people say that this game has much more similarity to Sonic Adventure 2 than Super Mario Galaxy. I'm confused as to how, in really any way?
Well at a stretch; the world map is more like a selection screen now and there are several levels that love to stick Sonic on rails much like SA2. Other than that, I'm with you.
Is it me, or does it seem like Sega's trying to phase humans out of Sonic's universe, given how we haven't seen any since Sonic Colors, and Sonic's "world" in Lost World (not the Lost Hex) looks a lot like the old games, with polygonal trees and whatnot...no, Eggman doesn't count as a human, since he's the classic villain in these titles.
I'm not sure if the 3DS version is canon, but I'll throw this out anyway. In the final boss in Lost World 3DS, enough hits free a Wisp. His mech is powered by Sonic's world's energy. How did they get there? Might the Wisps actually be part of the earth, supporting it, related to the Gaia? Furthermore, what else could the Wisps be a part of, and how long have they actually been on Sonic's world?
It was Comfirmed in Sonic Runners that some of the Wisps are going back to their home planet(Planet Wisp), while some others are staying. Maybe because they love to harnass Sonic's Hyper-go-on power?