Choices are always a good thing though, and plenty of fangames use it. Celestite is a good example of that: you can choose to play the straight hero, or join the bad guys. There's always the anti-hero route as well, which is a good middle ground.
So, they would basically act like Shadow Pokemon? I do like the idea of the Pokegear thing, it would make for a more immersive and unique experience. It's those little things that add up and help make a great game (like Persona 5's menu screen, the shop keepers' inventories, ect).
I do think we should shy away from having the typical "I'm a kid starting my journey" thing as well. Perhaps we can take an approach similar to Colosseum?
An no need to apologise! I'll be going to D&D soonish, and maybe I'll get an inspiration strike there ^^