Well they originally had a female role planned for Gen I but it got cut out due to limitations or something, so I wouldn't really say it's the same case. I doubt they'd change May and Brendan anyway due to them really being the first properly named protagonists(May also was a big part of the anime, unlike the females of the first 2 gens).
I also think the Moss rock, Cold rock, etc. will be included. Deep in Shoal Cave could be the location of the Cold Rock, Petalburg Woods could be the location of Moss Rock, and maybe New Mauville for the magnetic evolutions? The problem I see with the last one is how they'd have to prevent you from evolving Magneton(Magnemite are gotten there) if they don't intend on expanding the Dex to include new evos from the start.
As for Day/Night, they could be easily implemented because, although there was no real day/night, they could evolve depending on the time of day.
On another note, I hope the Battle Frontier facilities run in a similar way, just with the needed tweaks to bring it up-to-date.