>>41007772In the context of a game like this, doing it with the Poke Ball license makes the experience less linear. Suddenly, there's a reason to re-explore older areas if they have strong Pokemon in them.
Knowing everything I do about this game, they probably don't utilize it very well, but in concept the idea is sound anyway.
The thing about shinies is not really a big deal. It's not like the restriction will be in place by the time you'd be intentionally hunting for shinies anyway.