This is great news!
Getting one or the other for the logo bird isn't really a deal breaker, since I can't imagine how both wouldn't be in both games. If they removed one they would not only break the story, but also make either Whirl Islands or Burned Tower pointless in each game, since about the only point they serve is to house their bird (and a few items and random encounters).
Any Crystal features will probably not be present, considering this is a GS remake, not a Crystal remake. FR/LG didn't include Yellow updates for example, and they will most likely want to keep this a pure remake as well. If one thing from Crystal is remade I bet it's the Battle Tower. In that case, my bet is that the Trainer House in Viridian will be beefed up to something bigger. And Kanto will be present, I really dn't see how they could skip it, seeing as they would have to remove the train in Goldenrod, and a all in all a highly appreciated feature of the originals. About the only real news will probably be new move tutors, and a possible new post game area, like a new island, a beefed up Mt Silver area, or a Battle Frontier.
It will be interesting to see how they handle Headbutting Trees. A Move Tutor (possibly an infinite one) or more likely just replacing it with Honey Trees are the most probable scenarios.
Whirlpool is another interesting point, considering the whirlpools named the the area Whirl Islands. They can't really add whirlpool as a move tutor move either, since it would be deletable at any time, unlike a HM, which could potentially screw you up, and any new TMs or HMs are highly unlikely. They will most likely just create some other feature keeping you from entering it early, and add whirlpools as a mere graphical effect.
Gym leaders and Elite Four are also likely to be kept just the same as before,with new movesets of course, in order to maintain the closeness to the original. GS did have a bit shorter between gyms and the E4 than the other games, making their lower levels rather balanced, at least in my experience.
