Yeah... as Zowayix (and others!) said, the chance never was as high as 50/50 if you bred a shiny Pokemon, let alone two. The chances were improved, but that's down to how the game mechanics worked then - now, since they've changed I wouldn't expect it.
There's always the chance for the Odd Egg though (Pokemon egg given to you in Crystal on top of the Togepi egg which had the offspring (2d gen 'baby forms - e.g. Elekid) with Dizzy Punch and a 50% chance of being shiny), and there is a 'Mausda method' (sp?) which does somewhat increase the likelihood of breeding a shiny if you breed foriegn Pokemon - but nowhere
near a 1 in 64 chance, and that's done to further promote trading via the GTS, according to a game creator and all. Don't expect anything else from that, personally.
1.) Will we be able to cut grass again in this one? (In the color/metal gen you could cut the tall grass).
2.) Do you think they will do anything with the burned down Cinabar Island in this one?
3.)Stones! Evolutionary Stones were a pain, do you think they'll make them easier to find? And if they do, what will happen to Bill's grand-pappy?
Maybe, but I don't really think it'll happen... but hey, it's only a minor thing anyway, so who knows?
They may... it'll be interesting, have to say. I personally would be kinda iffy if they did pretend that never happened given it was a GSC thing, but I'd prefer if the Island was still... not so darn dull (seeing the volcano would be neat), and the same for the Seafoam Islands.
Stones... well, I personally believe they may go the Route Crystal did - in that some people, when they called you, would give you an item if you visited them on top of the possibility of a battle - some of those were the Stones. (And we know the phone function is back as well...). Since Bill's Grandfather still had the same role... maybe he'll continue having that as well. Wonder though if showing him the 4th gen Eevee-lutions does something, if he does return?