No he is just the creator of the creatures in this series, but by no means god. Its a silly fan mistake that's taken to proportions of ridiculous size. Anyway Silktree is the damn Unown research founder. The only hint HGSS has is the fact that they actually featured an area in a region that doesn't exist. YET.
There are no hints in HG/SS. There weren't any in Emerald, so why would there be in HG/SS? If anything, go look for gen V hints in Ranger Tracks of light, you'll have way more chance.
While not plot related...
HGSS had the perspective that B/W is using. It used it on the Lighthouse part, and you can hack the rom to use it elsewhere.
Have to wonder if they were using HGSS as a testing ground for that camera angle.
I know there was a blog someone at Game Freak did on how HGSS was the testing ground for the next gen. I just can't find it.
EDIT: Well, the foreign building is obviously a censored church. And the stained glass is of Mt. Coronet where the hall of origin is. So.. yeah, he might be worshipped.
Yeah I think it was one of Gamefreaks in Japanese that did say a lot of things were testing grounds. So I do wonder if it inculdes the unnamed land where the ruins are.
Whatever, its not canon that he's a god anyway.
Plus there's the Arceus events in HGSS, the Hall of Origin and Platinum...
Doesn't really get much more canon than that.
On another topic, the Grunt in Kanto mentioned that he would restart TR in his home region. It is interesting to note that this line was added in HGSS and was not in the original GSC.
Lastly, I would love for the Shinto ruins to be in the explorable region of B&W. It could help expand and flesh out the Johto region's myths as well as the Sinnoh myth (there's still a lot about it that we don't know).
Aside from that, and the perspective shift in the Olivine Lighthouse being the same one used in B&W, I really don't see any other possible hints of Gen V in HGSS
God I don't want Kanto again. Please no.