So I rewatched the episode Strange Attractors the day after it aired and haven't watched it since, but...

Am I remembering wrong that Samuel mentioned a "greater power" behind abilities when discussing with Tracy how it was to first discover her powers? If not, shoot me down, I won't mind, heh.

Outside of the first half of the first season or so Heroes has avoided much Lost-esque mystery style stuff. We had the symbols taking a prominent place for a while (Jessica's tattoo anyone?) and at the end of the second season the stuff in the Vault. (Which has never been explained either. Has it? Maybe one or two items have shown up that I've missed. Would have been nice if there'd been a Compass in there...) Beyond that, not much.

Is this mention of Samuel's an introduction to the Power behind the powers? Or just a smooth tongue trying to convince Tracy that he "understands?"

Personally, I'd prefer the latter, not wanting the show to have anything to do with gods or aliens or whatever it is they might have planned. But early in the show's history I remember the producers/writers intimating that there WOULD be a higher purpose behind abilities revealed.

So even without seeing the films, Samuel could sense the power specials emanate. Its not been stated flat out but I'm pretty sure he's the only one affected in this way, yeah? We didn't see anyone elses power at Coyote Sands go haywire.

I do hope they leave God(s) out of this. If they do use that "explanation" (Goddidit), it would contradict with the idea that they gained their abilities through natural selection.
And perhaps they are forgetting that not everybody actually believes in any God? Some fans wouldn't be too pleased, I'm sure.