What if Naraku created the well? He did put a black hole in someone's hand and can now teleport. From what physics theories I've read, time travel is along the same lines, so I doubt it's beyond his abilities.
Also, he had the motive to do it. In the fifty years he wandered around, he could've somehow found out that the Shikon Jewel was destined to reappear sometime in the distant future in the same place it left. It would make sense for him not to want to wait that long. He could've even been the one to send Mistress Centipede after it in the first place. (He didn't necessarily have to know who Kagome was or that she was Kikyou's reincarnation.)
It's odd, but if it were ever revealed to be true, what would that mean for Inu/Kag fans?? Would that mean they owe their meeting and relationship to Naraku, of all people? And could Naraku also travel through into her time if he wanted?
Whew! Okay, I feel better now.
So, anyone else got any crazy theories running around in their heads?
It would really tie a lot of things in the series together. Unfortunately, it doesn't sound at all like Takahashi's usual style (knowing her, the well is just sort of... random XD), because I'd love to see it happen. Even though it would probably mean bad things for our heroes, just because Naraku was able to make it wouldn't necessarily mean he'd be able to unmake it just as easily.