An alternate theory from here: The Homing Attack is a side effect of turning Hyper Sonic in the last game. In fact, look at the Chaos Emeralds; they're way bigger than in games further down the timeline, like Sonic Heroes or Shadow. They're still powering down from the power boost they got before. Which explains why Sonic's super form conks out in combo moves: they're not stabilized yet.
Badniks aren't exactly great challenges on their own, and even in groups they'll give moderate trouble at best. Metal Sonic has proven himself to be rather arrogant, and since his mission is to terminate Sonic it's likely that he is the only one Metal could possibly consider his rival. Therefore, he wouldn't waste his time and energy using his powers on the slow, clunky Badniks, but rather save them for when he has the world's fastest hedgehog to contend with.
It was said that Episode 2 would bridge a gap between Metal Sonic's appearance in CD and explain how he showed up in Heroes. At first, you see no allusions to Heroes, but then you realize that this isn't meant to be a direct link; this is meant to set up Metal Sonic's slip into madness. The best technology at their disposal, the strongest mystical energy they can find without resorting to Chaos energy, all weaved into his chassis, and he still can't manage a fight with Sonic. Add in the fact that someone even stronger than him showed up and allowed for such a close bout than the Doctor had gotten with Metal, and the mix of power corrupting his system, burning hatred, and a possible inferiority complex would eventually cause him to turn on his creator.
What if he claimed Metal Sonic and they left the Little Planet before time re-organised itself?
If Sonic had saved Stardust Speedway, Metal Sonic would have been defeated in the Good Future, with the Bad Future being untouched by Sonic as it never happened. That said, if time needed to reorganize itself, it would have been instantaneous in that case, Bad Future Metal Sonic would have been just fine... Alternately, Little Planet getting a Bad Future might have been a side effect of Time Eater's meddling, and since Sonic defeated Metal Sonic there too, your possibility opens up.
Remember that the final Bad Future was a catastrophe for Robotnik himself - all his machines out of control, Eggmanland logos destroyed, and so on. Perhaps Sonic DID fail to prevent Bad Future on the Little Planet (and who can blame him?), but Robotnik was dissatisfied with its results and simply left the planet corrupted after being defeated by Sonic.
So, in Ep. 2, Sonic and Tails got onto the Death Egg in a single pod, right? But when they left, they took two. Who did that second pod belong to, I wonder?
So, Sonic and Tails left after destroying the Heart, without which the Death Egg supposedly deactivated. And that's all. It's still around the Little Planet, and Robotnik can probably reactivate it sooner or later, one way or another. Perhaps that's it - perhaps the poor planet will become the Doctor's main base to launch new offensive on Sonic's world in the future?