The name "Broken Timeline" will probably be changed in the future to fit the new story better. As for the moment, BT is a temporary title name until either I can think of a more fitting one, or if I can connect the "timeline theme" to the new story. I'm betting on the latter though. :V
And with this reboot, the main character's background, history and story is entirely new, so he isn't a secret or amnesiac legendary this time. As for Chaomega, no, he won't be around until later.
Huh... You know, that's actually a very interesting idea. Four different colored keys might be a nice alternative to Mr. Box Opener if you're not willing to part 100 pokedollars. But then that would mean I'm going to sacrifice 4 OW sprites for that, and Ruby kinda has limited OW sprites. :/ But I'll consider it still, and I'll study how to do item scripts when I get the chance. :3
Your first few questions are identical to Feroniamon, so just check my reply to him/her. :3
As for your other questions... The region I chose is Crest, the region from SkyLine. So yeah, the game will focus on one region only.
For returning characters, I would say that that's not going to happen any time soon in the game. I originally made Crest an 'isolated little island region,' a bit far away from other larger regions, so technology is kinda slow to arrive there (hence why there's no PokéCenter).
For non-returning characters, I'd say the Dragon Gods won't be around because, well, in the LoG timeline, they died (except for one) while on the original timeline, Zah 'commanded' them, and after his defeat, well, the Dragons on his command disappeared with him. But who knows what'll happen after Chaomega merged the two timelines (yes, the two timelines merging is still a thing even in this BT reboot. But the game being before, during or after the merge, I'm not sure yet.)
So yeah...