My Thoughts:
Game Name/Mascot
Pokemon Gray/Grey or Pokemon Chrome. With Kyurem of course.
Wild Pokemon
I think Pokemon from earlier versions should be obtainable before completing the main story.
Striaton City Gym Battle
Instead of battling Bianca in Route 2 and battling Cheren in the Trainer School, you should be able to have a triple battle in the Striaton Gym: You, Cheren, and Bianca VS. Cilan, Chili, and Cress.
Reshiram and Zekrom
When you reach N at Dragonspiral Tower, he has obtained both.
Kyurem Battle
I have a suggestion. You can catch Kyurem after defeating the Opelucid City Gym. Go east to Lacunosa Town and you'll be able to. Now, this is where my suggestion comes in.
After you reach the giant hole, you travel back in time to the events of the Ice Age. I'd also think it's be nice if instead of having the Ice Age all blue and beautiful and icy-like, it should look gray/grey like a flashblack. In the Ice Age, you must have to go through a series of puzzles to reach Kyurem and catch him. Then you hear from an important character (a gym leader, Juniper, Cedric, etc.) that there is a powerful stone required to use Kyurem's full power. This is where you go through the Relic Castle and then Nacrene City, where Lenora gives you the God Stone. Here, Lenora should say "You cannot use this stone until the time is right." or something along those lines. (This time will be when you reach N at his castle). The God Stone shall give full power to Kyurem, revealing his true form.
Also, earlier I saw a suggestion. Somebody suggested that an area called Gray Mountains should replace Black City/White Forest. I really like this.