That sounds really interesting! I love games that utilize multiple choice stories and endings properly. It provides more replay value and makes the game more tuned the player. You also have a unique mechanic that sounds fun! The game sounds great and I can't wait to see it :).
Mine is very WIP. It takes place in Hoenn ~5 years after the events of R/S/E. I didn't feel confident enough introducing a new region because they are very hit or miss. Instead, I can introduce a few new characters but still have the older ones to work with. I enjoyed how in BW2 you could take on Cheren as a gym leader, Bianca was the professors assistant, etc.
I did however, wanted to introduce a new team which is part goon and part scientist. The guys higher up are doing the real work and the goons are just there to battle, much like Team Rocket, and basically every other team really... They are creating "spliced" Pokemon that are stronger and have less weakness, similar to what your team is doing I'm guessing.
Your main character is in his 20's. I wanted to make the experience a little bit more mature but still Pokemon like, because I guess that's what the demographic is for people who play fan games like these.